Novel deazapurines and uses thereof

ABSTRACT

The present invention provides methods of using compounds having formula (I):  
                 
 
     wherein R 1 , R 2 , R 3  and n are as described generally and in classes and subclasses herein, in the treatment of reperfusion injuries, osteoporosis and/or bone metastasis.

PRIORITY CLAIM

[0001] The present Application is a Continuation-In-Part and claims the benefit under 35 U.S.C. § 120 of co-pending International Application No.: PCT/US03/00366, filed Jan. 7, 2003 and published in English under PCT Article 21(2), which claims priority to U.S. Provisional Patent Application NO. 60/346,598, filed Jan. 7, 2002; the entire contents of each of these applications are incorporated herein by reference.

BACKGROUND OF THE INVENTION

[0002] Inflammation is a process resulting from the dilation and increased permeability of blood vessels at site of injury or infection. Chemokines and cytokines released at the site increase the expression of cell surface proteins on endothelial cells, allowing circulating leukocytes to stick to the vessel wall and migrate to the site of injury/infection within the tissue. These cell surface proteins, termed “cell adhesion molecules” allow the interaction between the leukocytes and the endothelial cells, and mediate the migration of leukocytes into the tissue. Additionally, cell adhesion molecules are required for many of the cell-to-cell interactions in the inflammatory and immune responses. There are three classes of adhesion molecules: selecting, integrins and immunoglobulin-related proteins which can be expressed on leukocytes and endothelial cells. Several of the adhesion molecules, including E-selectin and ICAM, are induced by cytokines such as IL-1 and TNF, and their expression is mediated by the transcriptional factor, NF-κB.

[0003] Sustained or inappropriate expression of adhesion molecules can lead to inflammatory or autoimmune disorders. Exaggerated expression of E-selectin and/or ICAM can result in chronic inflammation and has been associated with several inflammatory or autoimmune disorders. Therefore, inhibitors of cell adhesion molecules may be useful for the treatment of these diseases.

[0004] Inflammatory and autoimmune diseases are not well managed by current therapy and developments of better drugs are widely pursued. For example, rheumatoid arthritis is a state of chronic inflammation within the joint characterized by cartilage and bone destruction. Traditional therapies for inflammatory or autoimmune disease, such as rheumatoid arthritis, include nonsteroidal anti-inflammatory drugs and salicylates, gold compounds, hydroxychloroquine, sulfasalazine, corticosteroids, oral penicillamines, and cytotoxic or immunosuppressive drugs. However, many of these therapies are not always sufficiently effective and have resulted in serious side effects. More recently, injectable forms of TNFα neutralizing proteins have been successfully marketed for the treatment of rheumatoid arthritis and Crohn's Disease; however, an orally available inhibitor has not been developed for these inflammatory or autoimmune diseases.

[0005] Clearly, there remains a need to identify new classes of therapeutic agents for the treatment of inflammatory or autoimmune and proliferative diseases, preferably that are orally available, and are free of serious side effects. It would also be desirable to define new classes of therapeutic agents for the treatment of inflammatory or autoimmune and proliferative disorders in general.

SUMMARY OF THE INVENTION

[0006] As discussed above, there remains a need for the development of novel therapeutic agents useful for treating inflammatory or autoimmune and proliferative diseases. The present invention provides methods of using novel compounds of general formula (I),

[0007] and/or pharmaceutical compositions thereof, as described generally and in classes and subclasses herein, in the treatment of reperfusion injuries, osteoporosis and/or bone metastasis.

DESCRIPTION OF CERTAIN PREFERRED EMBODIMENTS OF THE INVENTION

[0008] In recognition of the need to investigate and define new classes of therapeutic agents for the treatment of rheumatoid arthritis and other disorders (in certain embodiments, inflammatory or autoimmune and proliferative disorders), the present invention provides novel deazapurines and analogues thereof, as described in more detail herein, which are useful generally in the treatment of inflammatory or autoimmune and proliferative disorders. In certain embodiments, the compounds of the present invention can be used for the treatment of diseases and disorders including, but not limited to, rheumatoid arthritis, ulcerative colitis/Crohn's disease, central nervous system diseases (CNS) such as multiple sclerosis, systemic lupus erythematosus, asthma, allograft rejection/graft versus host disease (GVHD), psoriasis, atopic dermatitis, eczema, uticaria, allergic rhinitis, myasthenia gravis, diabetes, idiopathic thrombocytopenia purpura, glomerulonephritis, cardiovascular disease, reperfusion injury, bone metastasis, bone resorption disorders, such as osteoporosis, and cancer.

1) General Description of Compounds of the Invention

[0009] The compounds of the invention include compounds of the general formula (I) (and tautomers thereof) as further defined below:

[0010] and pharmaceutically acceptable derivatives thereof;

[0011] wherein n is an integer from 0-4;

[0012] R₁ is hydrogen, —NH₂, —NHMe, —NHAc, —OH, F, —OMe, —CN, or —NH(C═O)OEt;

[0013] R₂ is hydrogen, —NR_(A)R_(B), —OR_(A), an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, wherein R_(A) and R_(B) are each independently hydrogen or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety;

[0014] each occurrence of R₃ is independently hydrogen, halogen, cyano, or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or a group —G—R_(C), wherein G is absent or is —CH₂—, —NR_(D)—, —O—, or (C═O), and wherein R_(C) is hydrogen, —NR_(FR) _(G), —OR_(F), —SR_(F), or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, wherein R_(D), R_(F) and R_(G) are each independently hydrogen, —NR_(x)R_(y), an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(D) and R_(C) or R_(F) and R_(G) taken together are a 3-, 4-, 5-, 6-, 7- or 8-membered substituted or unsubstituted cycloaliphatic or cycloheteroaliphatic moiety; wherein each occurrence of R_(x) and R_(y) is independently hydrogen, an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(x) and R_(y) taken together are a 4-, 5- or 6-membered substituted or unsubstituted, saturated or unsaturated cycloaliphatic or cycloheteroaliphatic moiety;

[0015] whereby each of the foregoing aliphatic or heteroaliphatic moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, saturated or unsaturated and wherein each of the foregoing aryl or heteroaryl moieties may be independently substituted or unsubstituted.

[0016] In certain embodiments, the present invention defines certain classes of compounds which are of special interest. For example, one class of compounds of special interest includes those compounds substituted with two occurrences of R₃ in which the compound has the structure:

[0017] wherein R_(3a) and R_(3b) are each independently hydrogen, halogen, cyano, or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or a group —G—R_(C), wherein G is absent, —CH₂—, —NR_(D)—, —O—, or (C═O), and wherein R_(C) is hydrogen, —NR_(F)R_(G), —OR_(F), —SR_(F), or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, wherein R_(D), R_(F) and R_(G) are each independently hydrogen, —NR_(x)R_(y), an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(D) and R_(C) or R_(F) and R_(G) taken together are a 3-, 4-, 5-, 6-, 7- or 8-membered substituted or unsubstituted cycloaliphatic or cycloheteroaliphatic moiety; wherein each occurrence of R_(x) and R_(y) is independently hydrogen, an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(x) and R_(y) taken together are a 4-, 5- or 6-membered substituted or unsubstituted, saturated or unsaturated cycloaliphatic or cycloheteroaliphatic moiety;

[0018] whereby each of the foregoing aliphatic or heteroaliphatic moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, saturated or unsaturated; and wherein each of the foregoing aryl or heteroaryl moieties may be independently substituted or unsubstituted.

[0019] Another class of compounds of special interest comprises compounds having the structure:

[0020] wherein R_(3a) and R_(3b) are each independently hydrogen, halogen, cyano, or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or a group —G—R_(C), wherein G is absent, —CH₂—, —NR_(D)—, —O—, or (C═O), and wherein R_(C) is hydrogen, —NR_(F)R_(G), —OR_(F), —SR_(F), or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, wherein R_(D), R_(F) and R_(G) are each independently hydrogen, —NR_(x)R_(y), an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(D) and R_(F) or R_(F) and R_(G) taken together are a 3-, 4-, 5-, 6-, 7- or 8-membered substituted or unsubstituted cycloaliphatic or cycloheteroaliphatic moiety; wherein each occurrence of R_(x) and R_(y) is independently hydrogen, an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(x) and R_(y) taken together are a 4-, 5- or 6-membered substituted or unsubstituted, saturated or unsaturated cycloaliphatic or cycloheteroaliphatic moiety;

[0021] whereby each of the foregoing aliphatic or heteroaliphatic moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, saturated or unsaturated; and wherein each of the foregoing aryl or heteroaryl moieties may be independently substituted or unsubstituted.

[0022] Another class of compounds of special interest comprises compounds having the structure of formula (I) in which R_(3a) is —CH₂NR_(F)R_(G) and R_(3b) is hydrogen and the compound has the structure:

[0023] wherein R₁, R₂, R_(F) and R_(C) are as defined generally above and in classes and subclasses herein.

[0024] Another class of compounds of special interest comprises compounds having the structure of formula (I) in which R_(3b) is —CH₂NR_(F)R_(G) and R_(3a) is hydrogen and the compound has the structure:

[0025] wherein R₁, R₂, R_(F) and R_(G) are as defined generally above and in classes and subclasses herein.

[0026] Another class of compounds of special interest comprises compounds having the structure of formula (I) in which R_(3c) is —CH₂NR_(F)R_(G) and R_(3d) is hydrogen and the compound has the structure:

[0027] wherein R₁, R₂, R_(F) and R_(G) are as defined generally above and in classes and subclasses herein.

[0028] Another class of compounds of special interest comprises compounds having the structure of formula (I) in which R_(3a) is —(CH═CH)_(q)CH₂(CH₂)_(r)NR_(F)R_(G) and R_(3b) is hydrogen and the compound has the structure:

[0029] wherein q and r are each independently 0 or 1; and R₁, R₂, R_(F) and R_(G) are as defined generally above and in classes and subclasses herein.

[0030] Another class of compounds of special interest comprises compounds having the structure of formula (I) in which R_(3a) is hydrogen and R_(3b) is —(CH═CH)_(q)CH₂(CH₂)_(r)NR_(F)R_(G) and the compound has the structure:

[0031] wherein q and r are each independently 0 or 1; and R₁, R₂, R_(F) and R_(G) are as defined generally above and in classes and subclasses herein.

[0032] Another class of compounds of special interest includes compounds having the structure of formula (I) in which R_(3a) is —(C═O)NR_(F)R_(G) and R_(3b) is hydrogen and the compound has the structure:

[0033] wherein R₁, R₂, R_(F) and R_(G) are as defined generally above and in classes and subclasses herein.

[0034] Another class of compounds of special interest includes compounds having the structure of formula (I) in which R_(3b) is —(C═O)NR_(F)R_(G) and R_(3a) is hydrogen and the compound has the structure:

[0035] wherein R₁, R₂, R_(F) and R_(G) are as defined generally above and in classes and subclasses herein.

[0036] Another class of compounds of special interest comprises compounds having the structure of formula (I) in which R_(3a) is —CH₂S(═O)_(m)NR_(F)R_(G) and R_(3b) is hydrogen and the compound has the structure:

[0037] wherein R₁ and R₂ are as defined generally above and in classes and subclasses herein;

[0038] m is 0, 1 or 2; and

[0039] R_(F) is an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety;

[0040] whereby each of the foregoing aliphatic or heteroaliphatic moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, saturated or unsaturated; and wherein each of the foregoing aryl or heteroaryl moieties may be independently substituted or unsubstituted.

[0041] Another class of compounds of special interest comprises compounds having the structure of formula (I) in which R_(3a) is —CH₂OR_(F) and R_(3b) is hydrogen and the compound has the structure:

[0042] wherein R₁ and R₂ are as defined generally above and in classes and subclasses herein; and

[0043] R_(F) is hydrogen, a protective group or an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety;

[0044] whereby each of the foregoing aliphatic or heteroaliphatic moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, saturated or unsaturated; and wherein each of the foregoing aryl or heteroaryl moieties may be independently substituted or unsubstituted.

[0045] A number of important subclasses of each of the foregoing classes deserve separate mention; these subclasses include subclasses of the foregoing classes in which:

[0046] i) R₁ is NH₂;

[0047] ii) R₁ is hydrogen;

[0048] iii) R₁ is NHMe;

[0049] iv) R₁ is NHAc;

[0050] v) R₂ is NH₂, OH, C₁-C₆ alkyl or C₁-C₆ alkenyl, said alkyl and alkenyl groups optionally substituted with halogen or hydroxyl;

[0051] vi) R₂ is C₁-C₂ alkyl;

[0052] vii) R₂ is methyl;

[0053] viii) R₂ is hydrogen;

[0054] ix) one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is an alkyl, heteroalkyl, aryl, heteroaryl, alkylaryl or alkylheteroaryl, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 6-membered substituted or unsubstituted heterocyclic moiety;

[0055] x) one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is an aryl, heteroaryl, alkylaryl or alkylheteroaryl moiety, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 6-membered substituted or unsubstituted cyclic or heterocyclic moiety;

[0056] xi) one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is phenyl, pyridyl, (alkyl)phenyl, or (alkyl)pyridyl, optionally substituted with one or more occurrences of halogen, trifluromethoxy, methoxy, trifluoromethyl, methylthio, or substituted or unsubstituted lower alkyl, lower heteroalkyl, aryl or heteroaryl; and

[0057] xii) one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is a cyclic or acyclic, linear or branched aliphatic moiety optionally substituted with one or more of substituted or unsubstituted aryl, heteroaryl, amide, alkoxy, hydroxyl, thioalkyl, thiol, acyl or amino;

[0058] xiii) R_(F) is an alkyl, cycloalkyl, heteroalkyl, cycloheteroalkyl, aryl, heteroaryl, alkylaryl or alkylheteroaryl, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl; and/or

[0059] xiv) R_(F) is hydrogen, a protecting group, or an alkyl, cycloalkyl, heteroalkyl, cycloheteroalkyl, aryl, heteroaryl, alkylaryl or alkylheteroaryl, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl.

[0060] As the reader will appreciate, compounds of particular interest include, among others, those which share the attributes of one or more of the foregoing subclasses. Some of those subclasses are illustrated by the following sorts of compounds:

I) Compounds of the Formula (and Pharmaceutically Acceptable Derivatives thereof)

[0061]

[0062] wherein R₁ and R₂ are as defined generically and in classes and subclasses herein; G is CH₂ or —(C═O) and one of R_(G) or R_(F) is hydrogen or lower alkyl; and the other is an alkyl, heteroalkyl, aryl, heteroaryl, alkylaryl or alkylheteroaryl moiety, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 3 to 8-membered substituted or unsubstituted cyclic or heterocyclic moiety.

[0063] In certain embodiments, one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is an aryl, heteroaryl, alkylaryl or alkylheteroaryl moiety, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 3 to 8-membered substituted or unsubstituted cyclic or heterocyclic moiety.

[0064] In certain other embodiments, one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is phenyl, pyridyl, (alkyl)phenyl, or (alkyl)pyridyl, optionally substituted with one or more occurrences of halogen, trifluromethoxy, methoxy, trifluoromethyl, methylthio, or substituted or unsubstituted lower alkyl, lower heteroalkyl, aryl or heteroaryl.

[0065] In still other embodiments, one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is a cyclic or acyclic, linear or branched aliphatic moiety optionally substituted with one or more of substituted or unsubstituted aryl, heteroaryl, amide, alkoxy, hydroxyl, thioalkyl, thiol, acyl or amino.

II) Compounds of the Formula (and Pharmaceutically Acceptable Derivatives thereof)

[0066]

[0067] wherein R₁ and R₂ are as defined generically and in classes and subclasses herein; G is CH₂ or —(C═O) and X is O, S, C═O, S═O, C═CR₄R₅, NR₄, or CR₄R₅; wherein each occurrence of R₄ and R₅ is independently hydrogen, hydroxyl, halogen, cyano an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, or is an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety;

[0068] whereby each of the foregoing aliphatic or heteroaliphatic moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, and wherein each of the foregoing aryl or heteroaryl moieties may be independently substituted or unsubstituted.

III) Compounds of the Formula (and Pharmaceutically Acceptable Derivatives thereof)

[0069]

[0070] wherein R₁ and R₂ are as defined generically and in classes and subclasses herein; G is CH₂ or —(C═O) and one of R_(G) or R_(F) is hydrogen or lower alkyl; and the other is an alkyl, heteroalkyl, aryl, heteroaryl, alkylaryl or alkylheteroaryl, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 3 to 8-membered substituted or unsubstituted cyclic or heterocyclic moiety.

[0071] In certain embodiments, one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is an aryl, heteroaryl, alkylaryl or alkylheteroaryl moiety, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 3 to 8-membered substituted or unsubstituted cyclic or heterocyclic moiety.

[0072] In certain other embodiments, one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is phenyl, pyridyl, (alkyl)phenyl, or (alkyl)pyridyl, optionally substituted with one or more occurrences of halogen, trifluromethoxy, methoxy, trifluoromethyl, methylthio, or substituted or unsubstituted lower alkyl, lower heteroalkyl, aryl or heteroaryl.

[0073] In still other embodiments, one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is a cyclic or acyclic, linear or branched aliphatic moiety optionally substituted with one or more of substituted or unsubstituted aryl, heteroaryl, amide, alkoxy, hydroxyl, thioalkyl, thiol, acyl or amino.

IV) Compounds of the Formula (and Pharmaceutically Acceptable Derivatives thereof)

[0074]

[0075] wherein R₁ and R₂ are as defined generically and in classes and subclasses herein; G is CH₂ or —(C═O) and X is O, S, C═O, S═O, C═CR₄R₅, NR₄, or CR₄R₅; wherein each occurrence of R₄ and R₅ is independently hydrogen, hydroxyl, halogen, cyano an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, or is an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety;

[0076] whereby each of the foregoing aliphatic or heteroaliphatic moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, and wherein each of the foregoing aryl or heteroaryl moieties may be independently substituted or unsubstituted.

V) Compounds of the Formula (and Pharmaceutically Acceptable Derivatives thereof)

[0077]

[0078] wherein R₁ and R₂ are as defined generically and in classes and subclasses herein; G is CH₂ or —(C═O) and one of R_(G) or R_(F) is hydrogen or lower alkyl; and the other is an alkyl, heteroalkyl, aryl, heteroaryl, alkylaryl or alkylheteroaryl, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 3 to 8-membered substituted or unsubstituted cyclic or heterocyclic moiety.

[0079] In certain embodiments, one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is an aryl, heteroaryl, alkylaryl or alkylheteroaryl moiety, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 3 to 8-membered substituted or unsubstituted cyclic or heterocyclic moiety.

[0080] In certain other embodiments, one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is phenyl, pyridyl, (alkyl)phenyl, or (alkyl)pyridyl, optionally substituted with one or more occurrences of halogen, trifluromethoxy, methoxy, trifluoromethyl, methylthio, or substituted or unsubstituted lower alkyl, lower heteroalkyl, aryl or heteroaryl.

[0081] In still other embodiments, one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is a cyclic or acyclic, linear or branched aliphatic moiety optionally substituted with one or more of substituted or unsubstituted aryl, heteroaryl, amide, alkoxy, hydroxyl, thioalkyl, thiol, acyl or amino.

VI) Compounds of the Formula (and Pharmaceutically Acceptable Derivatives thereof)

[0082]

[0083] wherein R₁ and R₂ are as defined generically and in classes and subclasses herein; G is CH₂ or —(C═O) and X is O, S, C═O, S═O, C═CR₄R₅, NR₄, or CR₄R₅; wherein each occurrence of R₄ and R₅ is independently hydrogen, hydroxyl, halogen, cyano an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, or is an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety;

[0084] whereby each of the foregoing aliphatic or heteroaliphatic moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, and wherein each of the foregoing aryl or heteroaryl moieties may be independently substituted or unsubstituted.

VII) Compounds of the Formula (and Pharmaceutically Acceptable Derivatives thereof)

[0085]

[0086] wherein R_(F), R₁ and R₂ are as defined generically and in classes and subclasses herein; p is an integer from 0-3; s is an integer from 0-4; A, B, D, E and each occurrence of K are independently absent, O, S, C═O, S═O, C═CR₄R₅, NR₄, or CR₄R₅, wherein each occurrence of R₄ and R₅ is independently hydrogen, hydroxyl, halogen, cyano, —OR_(x), —SR_(x), —NR_(x)R_(y), an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, or is an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety; and wherein A and B, B and D, D and E, E and K and any two adjacent K groups may be linked by a single or double bond as valency permits; wherein each occurrence of R_(x) and R_(y) is independently hydrogen, a protecting group, or an aliphatic, heteroaliphatic, aryl, heteroaryl, aliphaticaryl, heteroaliphatic aryl, aliphaticheteroaryl or heteroaliphaticheteroaryl moiety,

[0087] whereby each of the foregoing aliphatic or heteroaliphatic moieties may be independently substituted or unsubstituted, cyclic or acyclic, linear or branched, saturated or unsaturated and wherein each of the foregoing aryl, heteroaryl aliphaticaryl, heteroaliphatic aryl, aliphaticheteroaryl or heteroaliphaticheteroaryl moieties may be independently substituted or unsubstituted.

[0088] In certain exemplary embodiments,

[0089] represents a substituted or unsubstituted phenyl, pyridyl or furanyl moiety. In certain other embodiments,

[0090] represents a substituted or unsubstituted, saturated or unsaturated 3-, 4-, 5-, 6-, 7-, or 8-membered cycloalkyl or cycloheteroalkyl moiety. In certain exemplary embodiments,

[0091] represents substituted or unsubstituted cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl or cyclooctyl. In certain exemplary embodiments,

[0092] represents a substituted or unsubstituted bicyclic aliphatic moiety.

[0093] In certain exemplary embodiments, R_(F) is hydrogen or lower alkyl. In cerain embodiments, R_(F) is hydrogen or methyl.

[0094] It will also be appreciated that for each of the subgroups I-VII described above, a variety of other subclasses are of special interest, including, but not limited to those classes described above i)-xiv) and classes, subclasses and species of compounds described above and in the examples herein.

[0095] Some of the foregoing compounds can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., stereoisomers and/or diastereomers. Thus, inventive compounds and pharmaceutical compositions thereof may be in the form of an individual enantiomer, diastereomer or geometric isomer, or may be in the form of a mixture of stereoisomers. In certain embodiments, the compounds of the invention are enantiopure compounds. In certain other embodiments, a mixture of stereoisomers or diastereomers are provided.

[0096] Additionally, any and all tautomers of the foregoing compounds are encompassed by the invention. The invention is not limited to the tautomeric structures depicted herein. As but one example, compounds described and depicted generally as:

[0097] may also be described and depicted as:

[0098] Furthermore, certain compounds, as described herein may have one or more double bonds that can exist as either the Z or E isomer, unless otherwise indicated. The invention additionally encompasses the compounds as individual isomers substantially free of other isomers and alternatively, as mixtures of various isomers, e.g., racemic mixtures of stereoisomers. In addition to the above-mentioned compounds per se, this invention also encompasses pharmaceutically acceptable derivatives of these compounds and compositions comprising one or more compounds of the invention and one or more pharmaceutically acceptable excipients or additives.

[0099] Compounds of the invention may be prepared by crystallization of compound of formula (I) under different conditions and may exist as one or a combination of polymorphs of compound of general formula (I) forming part of this invention. For example, different polymorphs may be identified and/or prepared by using different solvents, or different mixtures of solvents for recrystallization; by performing crystallizations at different temperatures; or by using various modes of cooling, ranging from very fast to very slow cooling during crystallizations. Polymorphs may also be obtained by heating or melting the compound followed by gradual or fast cooling. The presence of polymorphs may be determined by solid probe NMR spectroscopy, IR spectroscopy, differential scanning calorimetry, powder X-ray diffractogram and/or other techniques. Thus, the present invention encompasses inventive compounds, their derivatives, their tautomeric forms, their stereoisomers, their polymorphs, their pharmaceutically acceptable salts their pharmaceutically acceptable solvates and pharmaceutically acceptable compositions containing them.

2) Compounds and Definitions

[0100] As discussed above, this invention provides novel compounds with a range of biological properties. Compounds of this invention have biological activities relevant for the treatment of inflammatory or autoimmune disorders and/or proliferative disorders. In certain embodiments, the compounds of the invention are useful for the treatment of rheumatoid arthritis, ulcerative colitis/Crohn's disease, central nervous system diseases (CNS) such as multiple sclerosis, systemic lupus erythematosus, asthma, allograft rejection/graft versus host disease (GVHD), psoriasis, atopic dermatitis, eczema, uticaria, allergic rhinitis, myasthenia gravis, diabetes, idiopathic thrombocytopenia purpura, glomerulonephritis, cardiovascular disease, reperfusion injury, bone metastasis, bone resorption disorders, such as osteoporosis, and cancer.

[0101] Compounds of this invention include those specifically set forth above and described herein, and are illustrated in part by the various classes, subgenera and species disclosed elsewhere herein.

[0102] Additionally, the present invention provides pharmaceutically acceptable derivatives of the inventive compounds, and methods of treating a subject using these compounds, pharmaceutical compositions thereof, or either of these in combination with one or more additional therapeutic agents. The phrase, “pharmaceutically acceptable derivative”, as used herein, denotes any pharmaceutically acceptable salt, ester, or salt of such ester, of such compound, or any other adduct or derivative which, upon administration to a patient, is capable of providing (directly or indirectly) a compound as otherwise described herein, or a metabolite or residue thereof. Pharmaceutically acceptable derivatives thus include among others pro-drugs. A pro-drug is a derivative of a compound, usually with significantly reduced pharmacological activity, which contains an additional moiety which is susceptible to removal in vivo yielding the parent molecule as the pharmacologically active species. An example of a pro-drug is an ester. which is cleaved in vivo to yield a compound of interest. Pro-drugs of a variety of compounds, and materials and methods for derivatizing the parent compounds to create the pro-drugs, are known and may be adapted to the present invention. Certain exemplary pharmaceutical compositions and pharmaceutically acceptable derivatives will be discussed in more detail herein below.

[0103] Certain compounds of the present invention, and definitions of specific functional groups are also described in more detail below. For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75^(th) Ed., inside cover, and specific functional groups are generally defined as described therein. Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in “Organic Chemistry”, Thomas Sorrell, University Science Books, Sausalito: 1999, the entire contents of which are incorporated herein by reference. Furthermore, it will be appreciated by one of ordinary skill in the art that the synthetic methods, as described herein, utilize a variety of protecting groups. By the term “protecting group”, has used herein, it is meant that a particular functional moiety, e.g., O, S, or N, is temporarily blocked so that a reaction can be carried out selectively at another reactive site in a multifunctional compound. In preferred embodiments, a protecting group reacts selectively in good yield to give a protected substrate that is stable to the projected reactions; the protecting group must be selectively removed in good yield by readily available, preferably nontoxic reagents that do not attack the other functional groups; the protecting group forms an easily separable derivative (more preferably without the generation of new stereogenic centers); and the protecting group has a minimum of additional functionality to avoid further sites of reaction. As detailed herein, oxygen, sulfur, nitrogen and carbon protecting groups may be utilized. For example, in certain embodiments, as detailed herein, certain exemplary oxygen protecting groups are utilized. These oxygen protecting groups include, but are not limited to methyl ethers, substituted methyl ethers (e.g., MOM (methoxymethyl ether), MTM (methylthiomethyl ether), BOM (benzyloxymethyl ether), PMBM (p-methoxybenzyloxymethyl ether), to name a few), substituted ethyl ethers, substituted benzyl ethers, silyl ethers (e.g., TMS (trimethylsilyl ether), TES (triethylsilylether), TIPS (triisopropylsilyl ether), TBDMS (t-butyldimethylsilyl ether), tribenzyl silyl ether, TBDPS (t-butyldiphenyl silyl ether), to name a few), esters (e.g., formate, acetate, benzoate (Bz), trifluoroacetate, dichloroacetate, to name a few), carbonates, cyclic acetals and ketals. In certain other exemplary embodiments, nitrogen protecting groups are utilized. These nitrogen protecting groups include, but are not limited to, carbamates (including methyl, ethyl and substituted ethyl carbamates (e.g., Troc), to name a few) amides, cyclic imide derivatives, N-Alkyl and N-Aryl amines, imine derivatives, and enamine derivatives, to name a few. Certain other exemplary protecting groups are detailed herein, however, it will be appreciated that the present invention is not intended to be limited to these protecting groups; rather, a variety of additional equivalent protecting groups can be readily identified using the above criteria and utilized in the present invention. Additionally, a variety of protecting groups are described in “Protective Groups in Organic Synthesis” Third Ed. Greene, T. W. and Wuts, P. G., Eds., John Wiley & Sons, New York: 1999, the entire contents of which are hereby incorporated by reference.

[0104] It will be appreciated that the compounds, as described herein, may be substituted with any number of substituents or functional moieties. In general, the term “substituted” whether preceded by the term “optionally” or not, and substituents contained in formulas of this invention, refer to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent. When more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. As used herein, the term “substituted” is contemplated to include all permissible substituents of organic compounds. In a broad aspect, the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and nonaromatic substituents of organic compounds. For purposes of this invention, heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valencies of the heteroatoms. Furthermore, this invention is not intended to be limited in any manner by the permissible substituents of organic compounds. Combinations of substituents and variables envisioned by this invention are preferably those that result in the formation of stable compounds useful in the treatment, for example of inflammatory or autoimmune and proliferative disorders, including, but not limited to rheumatoid arthritis, psoriasis, asthma and cancer. The term “stable”, as used herein, preferably refers to compounds which possess stability sufficient to allow manufacture and which maintain the integrity of the compound for a sufficientperiod of time to be detected and preferably for a sufficient period of time to be useful for the purposes detailed herein.

[0105] The term “aliphatic”, as used herein, includes both saturated and unsaturated, straight chain (i.e., unbranched), branched, cyclic, or polycyclic aliphatic hydrocarbons, which are optionally substituted with one or more functional groups. As will be appreciated by one of ordinary skill in the art, “aliphatic” is intended herein to include, but is not limited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties. Thus, as used herein, the term “alkyl” includes straight, branched and cyclic alkyl groups. An analogous convention applies to other generic terms such as “alkenyl”, “alkynyl” and the like. Furthermore, as used herein, the terms “alkyl”, “alkenyl”, “alkynyl” and the like encompass both substituted and unsubstituted groups. In certain embodiments, as used herein, “lower alkyl” is used to indicate those alkyl groups (cyclic, acyclic, substituted, unsubstituted, branched or unbranched) having 1-6 carbon atoms.

[0106] In certain embodiments, the alkyl, alkenyl and alkynyl groups employed in the invention contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-4 carbon atoms. Illustrative aliphatic groups thus include, but are not limited to, for example, methyl, ethyl, n-propyl, isopropyl, cyclopropyl, —CH₂-cyclopropyl, allyl, n-butyl, sec-butyl, isobutyl, tert-butyl, cyclobutyl, —CH₂-cyclobutyl, n-pentyl, sec-pentyl, isopentyl, tert-pentyl, cyclopentyl, —CH₂-cyclopentyl-n, hexyl, sec-hexyl, cyclohexyl, —CH₂-cyclohexyl moieties and the like, which again, may bear one or more substituents. Alkenyl groups include, but are not limited to, for example, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, and the like. Representative alkynyl groups include, but are not limited to, ethynyl, 2-propynyl (propargy1), 1-propynyl and the like.

[0107] The term “alkoxy” (or “alkyloxy”), or “thioalkyl” as used herein refers to an alkyl group, as previously defined, attached to the parent molecular moiety through an oxygen atom or through a sulfur atom. In certain embodiments, the alkyl group contains 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl group contains 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl group contains 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl group contains 1-4 aliphatic carbon atoms. Examples of alkoxy, include but are not limited to, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, tert-butoxy, neopentoxy and n-hexoxy. Examples of thioalkyl include, but are not limited to, methylthio, ethylthio, propylthio, isopropylthio, n-butylthio, and the like.

[0108] The term “alkylamino” refers to a group having the structure —NHR′wherein R′ is alkyl, as defined herein. The term “aminoalkyl” refers to a group having the structure NH₂R′—, wherein R′ is alkyl, as defined herein. In certain embodiments, the alkyl group contains 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl group contains 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl group contains 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl group contains 1-4 aliphatic carbon atoms. Examples of alkylamino include, but are not limited to, methylamino, ethylamino, iso-propylamino and the like.

[0109] Some examples of sutstituents of the above-described aliphatic (and other) moieties of compounds of the invention include, but are not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; alkylaryl; alkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH; —CH₂NH₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x) wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, or alkylheteroaryl, wherein any of the aliphatic, heteroaliphatic, alkylaryl, or alkylheteroaryl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substituents are illustrated by the specific embodiments shown in the Examples that are described herein.

[0110] In general, the terms “aryl” and “heteroaryl”, as used herein, refer to stable mono- or polycyclic, heterocyclic, polycyclic, and polyheterocyclic unsaturated moieties having preferably 3-14 carbon atoms, each of which may be substituted or unsubstituted. It will also be appreciated that aryl and heteroaryl moieties, as defined herein may be attached via an aliphatic, heteroaliphatic, alkyl or heteroalkyl moiety and thus also include -(aliphatic)aryl, -(heteroaliphatic)aryl, -(aliphatic)heteroaryl, -(heteroaliphatic)heteroaryl, -(alkyl)aryl, -(heteroalkyl)aryl, -(heteroalkyl)aryl, and -(heteroalkyl)heteroaryl moieties. Thus, as used herein, the phrases “aryl or heteroaryl” and “aryl, heteroaryl, -(aliphatic)aryl, -(heteroaliphatic)aryl, -(aliphatic)heteroaryl, -(heteroaliphatic)heteroaryl, -(alkyl)aryl, -(heteroalkyl)aryl, -(heteroalkyl)aryl, and -(heteroalkyl)heteroaryl” are interchangeable. Substituents include, but are not limited to, any of the previously mentioned substitutents, i.e., the substituents recited for aliphatic moieties, or for other moieties as disclosed herein, resulting in the formation of a stable compound. In certain embodiments of the present invention, “aryl” refers to a mono- or bicyclic carbocyclic ring system having one or two aromatic rings including, but not limited to, phenyl, naphthyl, tetrahydronaphthyl, indanyl, indenyl and the like. In certain embodiements of the present invention, the term “heteroaryl”, as used herein, refers to a cyclic aromatic radical having from five to ten ring atoms of which one ring atom is selected from S, O and N; zero, one or two ring atoms are additional heteroatoms independently selected from S, O and N; and the remaining ring atoms are carbon, the radical being joined to the rest of the molecule via any of the ring atoms, such as, for example, pyridyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, and the like.

[0111] It will be appreciated that aryl and heteroaryl groups (including bycyclic aryl groups) can be unsubstituted or substituted, wherein substitution includes replacement of one, two or three of the hydrogen atoms thereon independently with any one or more of the following moieties including, but not limited to: aliphatic; heteroaliphatic; aryl; heteroaryl; alkylaryl; alkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH; —CH₂NH₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x) wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, or alkylheteroaryl, wherein any of the aliphatic, heteroaliphatic, alkylaryl, or alkylheteroaryl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substituents are illustrated by the specific embodiments shown in the Examples that are described herein.

[0112] The term “cycloalkyl”, as used herein, refers specifically to groups having three to seven, preferably three to ten carbon atoms. Suitable cycloalkyls include, but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and the like, which, as in the case of other aliphatic, heteroaliphatic or hetercyclic moieties, may optionally be substituted with substituents including, but not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; alkylaryl; alkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH; —CH₂NH₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x) wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, or alkylheteroaryl, wherein any of the aliphatic, heteroaliphatic, alkylaryl, or alkylheteroaryl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substituents are illustrated by the specific embodiments shown in the Examples that are described herein.

[0113] The term “heteroaliphatic”, as used herein, refers to aliphatic moieties which contain one or more oxygen sulfur, nitrogen, phosphorus or silicon atoms, e.g., in place of carbon atoms. Heteroaliphatic moieties may be branched, unbranched, cyclic or acyclic and include saturated and unsaturated heterocycles such as morpholino, pyrrolidinyl, etc. In certain embodiments, heteroaliphatic moieties are substituted by independent replacement of one or more of the hydrogen atoms thereon with one or more moieties including, but not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; alkylaryl; alkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH; —CH₂NH₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x) wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, or alkylheteroaryl, wherein any of the aliphatic, heteroaliphatic, alkylaryl, or alkylheteroaryl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substituents are illustrated by the specific embodiments shown in the Examples that are described herein.

[0114] The terms “halo” and “halogen” as used herein refer to an atom selected from fluorine, chlorine, bromine and iodine.

[0115] The term “haloalkyl” denotes an alkyl group, as defined above, having one, two, or three halogen atoms attached thereto and is exemplified by such groups as chloromethyl, bromoethyl, trifluoromethyl, and the like.

[0116] The term “heterocycloalkyl” or “heterocycle”, as used herein, refers to a non-aromatic 5-, 6- or 7-membered ring or a polycyclic group, including, but not limited to a bi- or tri-cyclic group comprising fused six-membered rings having between one and three heteroatoms independently selected from oxygen, sulfur and nitrogen, wherein (i) each 5-membered ring has 0 to 1 double bonds and each 6-membered ring has 0 to 2 double bonds, (ii) the nitrogen and sulfur heteroatoms may be optionally be oxidized, (iii) the nitrogen heteroatom may optionally be quaternized, and (iv) any of the above heterocyclic rings may be fused to a benzene ring. Representative heterocycles include, but are not limited to, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, and tetrahydrofuryl. In certain embodiments, a “substituted heterocycloalkyl or heterocycle” group is utilized and as used herein, refers to a heterocycloalkyl or heterocycle group, as defined above, substituted by the independent replacement of one, two or three of the hydrogen atoms thereon with but are not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; alkylaryl; alkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂CH₂OH; —CH₂NH₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x) wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, aryl, heteroaryl, alkylaryl, or alkylheteroaryl, wherein any of the aliphatic, heteroaliphatic, alkylaryl, or alkylheteroaryl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substitutents described above and herein may be substituted or unsubstituted. Additional examples or generally applicable substituents are illustrated by the specific embodiments shown in the Examples which are described herein.

3) Research Uses, Formulation and Administration

[0117] According to the present invention, the inventive compounds may be assayed in any of the available assays known in the art for identifying compounds having a pre-determined biological activity. For example, the assay may be cellular or non-cellular, in vivo or in vitro, high- or low-throughput format, etc. In certain exemplary embodiments, the inventive compounds are tested in assays to identify those compounds having antiproliferative/anticancer activity, inflammatory cytokine signaling pathway inhibitory activity, adhesion molecule expression inhibitory activity and/or anti-inflammatory effect.

[0118] Thus, in one aspect, compounds of this invention which are of particular interest include those which:

[0119] exhibit activity generally as inhibitors of adhesion molecule expression on the endothelial cell surface upon stimulation with inflammatory cytokines;

[0120] exhibit activity as inhibitors of inflammatory cytokine signaling pathway;

[0121] exhibit an anti-inflammatory effect on suitable cell lines maintained in vitro, or in animal studies using a scientifically acceptable model;

[0122] exhibit an antiproliferative and/or anticancer effect on suitable cell lines maintained in vitro, or in animal studies using a scientifically acceptable model; and

[0123] exhibit a favorable therapeutic profile (e.g., safety, efficacy, and stability).

[0124] As discussed herein, compounds of the invention have been shown to reduce activation of the transcriptional factor NF-κB and inhibit the transcriptional activation in inflammatory cytokine signaling pathways, which regulates many genes such as IL-1α and TNF α involved in the pathology of several inflammatory diseases. For example, elevated levels of TNF α and/or IL-1 over basal levels have been implicated in mediating or exacerbating a number of disease states including rheumatoid arthritis; Pagets disease; osteoporosis; multiple myeloma; uveititis; acute and chronic myelogenous leukemia; pancreatic B cell destruction; osteoarthritis; rheumatoid spondylitis; gouty arthritis; inflammatory bowel disease; adult respiratory distress syndrome (ARDS); psoriasis; Crohn's disease; allergic rhinitis; ulcerative colitis; anaphylaxis; contact dermatitis; asthma; muscle degeneration; cachexia; Reiter's syndrome; type I and type II diabetes; bone resorption diseases; graft vs. host reaction; ischemia reperfusion injury; atherosclerosis; brain trauma; multiple sclerosis; cerebral malaria; sepsis; septic shock; toxic shock syndrome; fever, and myalgias due to infection. HIV-1,HIV-2,HIV-3, cytomegalovirus (CMV), influenza, adenovirus, the herpes viruses (including HSV-1,HSV-2), and herpes zoster are also exacerbated by TNF α.

[0125] Certain compounds as described herein exhibit activity generally as inhibitors of cell adhesion molecules on endothelial cells (E-selectin and ICAM) and transcriptional activation induced by inflammatory cytokine signaling. More specifically, compounds of the invention demonstrate immunomodulatory activity and thus the invention further provides a method for treating an inflammatory or autoimmune disorder or a proliferative disorder. In certain embodiments, the inventive compounds as useful for the treatment of rheumatoid arthritis, ulcerative colitis/Crohn's disease, central nervous system diseases (CNS) such as multiple sclerosis, systemic lupus erythematosus, asthma, allograft rejection/graft versus host disease (GVHD), psoriasis, atopic dermatitis, eczema, uticaria, allergic rhinitis, myasthenia gravis, diabetes, idiopathic thrombocytopenia purpura, glomerulonephritis, cardiovascular disease, reperfusion injury, bone metastasis, bone resorption disorders, such as osteoporosis, and cancer.

[0126] As mentioned above, compounds of the invention have been shown to inhibit adhesion molecule expression such as E-selectin and ICAM-1 on the endothelial cell surface induced by stimulation with inflammatory cytokines. Accordingly, compounds of the invention may be useful for the treatment or prophylaxis of diseases caused by expression of adhesion molecules. These diseases include those in which leukocyte trafficking plays a role, notably acute and chronic inflammatory diseases, autoimmune diseases, tumor metastasis, allograft rejection, and reperfusion injury.

[0127] Therefore, in certain embodiments, compounds of the invention may be useful for the treatment of any one or more of the above-mentioned diseases or conditions. In certain exemplary embodiments, compounds of the invention are useful for treating or lessening the severity of disorders selected from reperfusion injury, bone metastasis and/or bone resorption disorders, such as osteoporosis.

[0128] Reperfusion Injury

[0129] Tissues deprived of blood and oxygen undergo ischemic necrosis or infarction with possible irreversible organ damage. In some circumstances, however, such as during cardiac surgery, it is desirable to interrupt the normal myocardial contractions (cardioplegia) and actually induce ischemia. Such elective or obligatory ischemia occurs in the presence of safeguards such as cardioplegia-induced cardiac arrest and hypothermia. While these safeguards provide considerable myocardial protection, alteration of myocardial energetics (stunning) and poor postoperative ventricular function still remain significant problems.

[0130] Once the flow of blood and oxygen is restored to the organ or tissue (reperfusion), the organ does not immediately return to the normal preischemic state. For example, reperfused postischemic non-necrotic myocardium is poorly contractile and has reduced concentrations of high energy nucleotides, depressed subcellular organelle function and membrane damage that resolves only slowly. Although reperfusion restores oxygen and reverses ischemia, repletion of high energy nucleotides such as adenosine triphosphate (ATP) and reversal of ischemic membrane damage is slow, and contractile function may be profoundly depressed for a long period. Just minutes of ischemia causes loss of myocardial systolic wall thickening for hours. Longer periods of reversible ischemia may depress contractility for days.

[0131] In certain exemplary embodiments, compounds of the invention are useful for treatment of stroke, cardiac, brain and/or renal reperfusion injury.

[0132] Bone Metastasis

[0133] Although the success rate for curing primary cancers is increasing, metastasis remains a limiting factor in antitumour therapy. Metastasis involves the spread of cancer cells from the primary cancer site to a secondary location elsewhere in the body. A common secondary site for metastasising tumour cells is in the bone. The presence of malignant cells in bone induces metabolic bone disease leading, for example, to bone resorption. The clinical symptoms of bone metastasis such as bone pain are partly linked to bone resorption. In advanced metastatic bone disease, the patient experiences excruciating pain due to pressure of the tumor on surrounding nerves, tissue, and the innervation of the bone and endosteum or periosteum itself. The quality of the patient's life at this point can deteriorate quickly, and the levels of pain become intolerable. In certain embodiments, compounds of the invention are useful for the treatment of bone metastases and/or are useful therapeutic agents for relieving bone pain in patients suffering from bone metastasis.

[0134] Pharmaceutical Compositions

[0135] As discussed above this invention provides novel compounds that have biological properties useful for the treatment of inflammatory and proliferative disorders, including, but not limited to rheumatoid arthritis, ulcerative colitis/Crohn's disease, central nervous system diseases (CNS) such as multiple sclerosis, systemic lupus erythematosus, asthma, allograft rejection/graft versus host disease (GVHD), psoriasis, atopic dermatitis, eczema, uticaria, allergic rhinitis, myasthenia gravis, diabetes, idiopathic thrombocytopenia purpura, glomerulonephritis, cardiovascular disease, reperfusion injury, bone metastasis, bone resorption disorders, such as osteoporosis, and cancer.

[0136] Accordingly, in another aspect of the present invention, pharmaceutical compositions are provided, which comprise any one or more of the compounds described herein (or a prodrug, pharmaceutically acceptable salt or other pharmaceutically acceptable derivative thereof), and optionally comprise a pharmaceutically acceptable carrier. In certain embodiments, a pharmaceutical composition comprising an inventive compound (or a prodrug, pharmaceutically acceptable salt or other pharmaceutically acceptable derivative thereof), a carrier or diluent and optionally an additional therapeutic agent is provided. In certain embodiments, compositions of the invention optionally further comprise one or more additional therapeutic agents. Alternatively, a compound of this invention may be administered to a patient in need thereof in combination with the administration of one or more other therapeutic agents. For example, additional therapeutic agents for conjoint administration or inclusion in a pharmaceutical composition with a compound of this invention may be an anti-inflammatory agent (e.g., an agent for the treatment of rheumatoid arthritis or psoriasis) or cytotoxic agent or anticancer agent approved for the treatment of cancer, as discussed in more detail herein, or it may be any one of a number of agents undergoing approval in the Food and Drug Administration that ultimately obtain approval for the treatment of an immune disorder or cancer. It will also be appreciated that certain of the compounds of present invention can exist in free form for treatment, or where appropriate, as a pharmaceutically acceptable derivative thereof. According to the present invention, a pharmaceutically acceptable derivative includes, but is not limited to, pharmaceutically acceptable salts, esters, salts of such esters, or a prodrug or other adduct or derivative of a compound of this invention which upon administration to a patient in need is capable of providing, directly or indirectly, a compound as otherwise described herein, or a metabolite or residue thereof.

[0137] As used herein, the term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts of amines, carboxylic acids, and other types of compounds, are well known in the art. For example, S. M. Berge, et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 66: 1-19 (1977), incorporated herein by reference. The salts can be prepared in situ during the final isolation and purification of the compounds of the invention, or separately by reacting a free base or free acid function with a suitable reagent, as described generally below. For example, a free base function can be reacted with a suitable acid. Furthermore, where the compounds of the invention carry an acidic moiety, suitable pharmaceutically acceptable salts thereof may, include metal salts such as alkali metal salts, e.g. sodium or potassium salts; and alkaline earth metal salts, e.g. calcium or magnesium salts. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hernisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate and aryl sulfonate.

[0138] Additionally, as used herein, the term “pharmaceutically acceptable ester” refers to esters that hydrolyze in vivo and include those that break down readily in the human body to leave the parent compound or a salt thereof. Suitable ester groups include, for example, those derived from pharmaceutically acceptable aliphatic carboxylic acids, particularly alkanoic, alkenoic, cycloalkanoic and alkanedioic acids, in which each alkyl or alkenyl moiety advantageously has not more than 6 carbon atoms. Examples of particular esters include formates, acetates, propionates, butyrates, acrylates and ethylsuccinates.

[0139] Furthermore, the term “pharmaceutically acceptable prodrugs” as used herein refers to those prodrugs of the compounds of the present invention which are, within the scope of sound medical judgment, suitable for use in contact with the issues of humans and lower animals with undue toxicity, irritation, allergic response, and the like, commensurate with a reasonable benefit/risk ratio, and effective for their intended use, as well as the zwitterionic forms, where possible, of the compounds of the invention. The term “prodrug” refers to compounds that are rapidly transformed in vivo to yield the parent compound of the above formula, for example by hydrolysis in blood. A thorough discussion is provided in T. Higuchi and V. Stella, Pro-drugs as Novel Delivery Systems, Vol. 14 of the A.C.S. Symposium Series, and in Edward B. Roche, ed., Bioreversible Carriers in Drug Design, American Pharmaceutical Association and Pergamon Press, 1987, both of which are incorporated herein by reference.

[0140] As described above, the pharmaceutical compositions of the present invention additionally comprise a pharmaceutically acceptable carrier, which, as used herein, includes any and all solvents, diluents, or other liquid vehicle, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980) discloses various carriers used in formulating pharmaceutical compositions and known techniques for the preparation thereof. Except insofar as any conventional carrier medium is incompatible with the compounds of the invention, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other component(s) of the pharmaceutical composition, its use is contemplated to be within the scope of this invention. Some examples of materials which can serve as pharmaceutically acceptable carriers include, but are not limited to, sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatine; talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; safflower oil, sesame oil; olive oil; corn oil and soybean oil; glycols; such as propylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogenfree water; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non-toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the composition, according to the judgment of the formulator.

[0141] Uses and Formulations of Compounds of the Invention

[0142] As described in more detail herein, in general, the present invention provides compounds useful for the treatment of inflammatory or autoimmune disorders and the treatment of proliferative disorders. Without wishing to be bound by any particular theory, more generally, the compounds of the invention have been shown to inhibit adhesion molecule expression such as E-selectin and ICAM-1 on the endothelial cell surface induced by stimulation with inflammatory cytokines. Such cell surface molecules play a critical role for inflammatory cell infiltration and cell-cell interactions within inflammatory and immune responses. The compounds also reduce activation of the transcriptional factor NF-κB and inhibit the transcriptional activation in inflammatory cytokine signaling pathways, which regulates many genes such as IL-1α and TNF α involved in the pathology of several inflammatory diseases. More generally, the identification of NF-κB as a key player in the pathogenesis of inflammation suggest that NF-κB targeted therapeutics may be effective in inflammatory and immune disorders (see, generally, NF-κB in Defense and Disease, J. Clin. Investig. 2001, 107, 7).

[0143] As detailed in the exemplification herein in assays to determine the ability of compounds to inhibit cytokine-induced adhesion molecule expression by endothelial cells, certain inventive compounds, (generally where one occurrence of R₃ is hydrogen, and the other occurrence of R₃ is a moiety as described generally herein) exhibited IC₅₀ values (E-Selectin and ICAM-1) less than 1 μM. In other embodiments, exemplary compounds exhibited IC₅₀ values less than 10 μM.

[0144] As discussed above, compounds of the invention exhibit immunomodulatory activity and exhibit activity for the inhibition of tumor cell growth. As such, compounds of the invention are particularly useful for the treatment of diseases and disorders including, but not limited to, rheumatoid arthritis, ulcerative colitis/Crohn's disease, central nervous system diseases (CNS) such as multiple sclerosis, systemic lupus erythematosus, asthma, allograft rejection/graft versus host disease (GVHD), psoriasis, atopic dermatitis, eczema, uticaria, allergic rhinitis, myasthenia gravis, diabetes, idiopathic thrombocytopenia purpura, glomerulonephritis, cardiovascular disease, reperfusion injury, bone metastasis, bone resorption disorders, such as osteoporosis, and cancer.

[0145] Thus, as described above, in another aspect of the invention, methods for the treatment of inflammatory or autoimmune and proliferative disorders are provided comprising administering a therapeutically effective amount of a compound of formula (I), or pharmaceutical composition thereof, as described herein, to a subject in need thereof. In certain embodiments, the inventive compounds are useful for the treatment of rheumatoid arthritis, ulcerative colitis/Crohn's disease, central nervous system diseases (CNS) such as multiple sclerosis, systemic lupus erythematosus, asthma, allograft rejection/graft versus host disease (GVHD), psoriasis, atopic dermatitis, eczema, uticaria, allergic rhinitis, myasthenia gravis, diabetes, idiopathic thrombocytopenia purpura, glomerulonephritis, cardiovascular disease, reperfusion injury, bone metastasis, bone resorption disorders, such as osteoporosis, and cancer.

[0146] In certain embodiments, there is provided a method for treating or lessening the severity of reperfusion injury comprising administering a therapeutically effective amount of an inventive compound (or a prodrug, pharmaceutically acceptable salt or other pharmaceutically acceptable derivative thereof), or pharmaceutical composition thereof, to a subject (including, but not limited to a human or animal) in need of it.

[0147] In certain embodiments, there is provided a method for treating or lessening the severity of a bone resorption disorder, such as osteoporosis, comprising administering a therapeutically effective amount of an inventive compound (or a prodrug, pharmaceutically acceptable salt or other pharmaceutically acceptable derivative thereof), or pharmaceutical composition thereof, to a subject (including, but not limited to a human or animal) in need of it.

[0148] In certain embodiments, there is provided a method for treating or lessening the severity of bone metastasis comprising administering a therapeutically effective amount of an inventive compound (or a prodrug, pharmaceutically acceptable salt or other pharmaceutically acceptable derivative thereof), or pharmaceutical composition thereof, to a subject (including, but not limited to a human or animal) in need of it.

[0149] In certain embodiments, the method involves the administration of a therapeutically effective amount of a compound of the invention (or a prodrug, pharmaceutically acceptable salt or other pharmaceutically acceptable derivative thereof), or pharamceutical composition thereof, and an additional therapeutic agent.

[0150] It will be appreciated that the compounds and compositions, according to the method of the present invention, may be administered using any amount and any route of administration effective for the treatment of inflammatory or autoimmune and proliferative disorders. Thus, the expression “effective amount” as used herein, refers to a sufficient amount of agent to kill or inhibit the growth of tumor cells, or refers to a sufficient amount to reduce the effects of an inflammatory or autoimmune response or disorder. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular therapeutic agent, its mode of administration, and the like. The compounds of the invention are preferably formulated in dosage unit form for ease of administration and uniformity of dosage. The expression “dosage unit form” as used herein refers to a physically discrete unit of therapeutic agent appropriate for the patient to be treated. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed; and like factors well known in the medical arts (see, for example, Goodman and Gilman's, “The Pharmacological Basis of Therapeutics”, Tenth Edition, A. Gilman, J. Hardman and L. Limbird, eds., McGraw-Hill Press, 155-173, 2001, which is incorporated herein by reference in its entirety).

[0151] Furthermore, after formulation with an appropriate pharmaceutically acceptable carrier in a desired dosage, the pharmaceutical compositions of this invention can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated. In certain embodiments, the compounds of the invention may be administered at dosage levels of about 0.001 mg/kg to about 50 mg/kg, from about 0.01 mg/kg to about 25 mg/kg, or from about 0.1 mg/kg to about 10 mg/kg of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect. It will also be appreciated that dosages smaller than 0.001 mg/kg or greater than 50 mg/kg (for example 50-100 mg/kg) can be administered to a subject. In certain embodiments, compounds are administered orally or parenterally.

[0152] Liquid dosage forms for oral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active compounds, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofIrfiryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.

[0153] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S.P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.

[0154] The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.

[0155] In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension or crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution that, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the drug in biodegradable polymers such as polylactide-polyglycolide. Depending upon the ratio of drug to polymer and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include (poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissues.

[0156] Compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.

[0157] Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar—agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may also comprise buffering agents.

[0158] Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.

[0159] The active compounds can also be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active compound may be admixed with at least one inert diluent such as sucrose, lactose and starch. Such dosage forms may also comprise, as in normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such as magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes.

[0160] Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches. The active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulation, ear drops, and eye drops are also contemplated as being within the scope of this invention. Additionally, the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms are made by dissolving or dispensing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.

[0161] It will also be appreciated that the compounds and pharmaceutical compositions of the present invention can be formulated and employed in combination therapies, that is, the compounds and pharmaceutical compositions can be formulated with or administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. The particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved. It will also be appreciated that the therapies employed may achieve a desired effect for the same disorder (for example, an inventive compound may be administered concurrently with another anti-inflammatory agent or anticancer agent), or they may achieve different effects (e.g., control of any adverse effects).

[0162] For example, other therapies or anticancer agents that may be used in combination with the inventive compounds of the present invention include surgery, radiotherapy (in but a few examples, γ-radiation, neutron beam radiotherapy, electron beam radiotherapy, proton therapy, brachytherapy, and systemic radioactive isotopes, to name a few), endocrine therapy, biologic response modifiers (interferons, interleukins, and tumor necrosis factor (TNF) to name a few), hyperthermia and cryotherapy, agents to attenuate any adverse effects (e.g., antiemetics), and other approved chemotherapeutic drugs, including, but not limited to, alkylating drugs (mechlorethamine, chlorambucil, Cyclophosphamide, Melphalan, Ifosfamide), antimetabolites (Methotrexate), purine antagonists and pyrimidine antagonists (6-Mercaptopurine, 5-Fluorouracil, Cytarabile, Gemcitabine), spindle poisons (Vinblastine, Vincristine, Vinorelbine, Paclitaxel), podophyllotoxins (Etoposide, Irinotecan, Topotecan), antibiotics (Doxorubicin, Bleomycin, Mitomycin), nitrosoureas (Carmustine, Lomustine), inorganic ions (Cisplatin, Carboplatin), enzymes (Asparaginase), and hormones (Tamoxifen, Leuprolide, Flutamide, and Megestrol), to name a few. For a more comprehensive discussion of updated cancer therapies see, The Merck Manual, Seventeenth Ed. 1999, the entire contents of which are hereby incorporated by reference. See also the National Cancer Institute (NCI) website (www.nci.nih.gov) and the Food and Drug Administration (FDA) website for a list of the FDA approved oncology drugs (www.fda.gov/cder/cancer/druglistframe—See Appendix A).

[0163] In certain embodiments, the pharmaceutical compositions of the present invention further comprise one or more additional therapeutically active ingredients (e.g., chemotherapeutic and/or palliative). For purposes of the invention, the term “Palliative” refers to treatment that is focused on the relief of symptoms of a disease and/or side effects of a therapeutic regimen, but is not curative. For example, palliative treatment encompasses painkillers, antinausea medications and anti-sickness drugs. In addition, chemotherapy, radiotherapy and surgery can all be used palliatively (that is, to reduce symptoms without going for cure; e.g., for shrinking tumors and reducing pressure, bleeding, pain and other symptoms of cancer).

TREATMENT KITS

[0164] In other embodiments, the present invention relates to a kit for conveniently and effectively carrying out the methods in accordance with the present invention. In general, the pharmaceutical pack or kit comprises one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. Such kits are especially suited for the delivery of solid oral forms such as tablets or capsules. Such a kit preferably includes a number of unit dosages, and may also include a card having the dosages oriented in the order of their intended use. If desired, a memory aid can be provided, for example in the form of numbers, letters, or other markings or with a calendar insert, designating the days in the treatment schedule in which the dosages can be administered. Alternatively, placebo dosages, or calcium dietary supplements, either in a form similar to or distinct from the dosages of the pharmaceutical compositions, can be included to provide a kit in which a dosage is taken every day. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceutical products, which notice reflects approval by the agency of manufacture, use or sale for human administration.

EQUIVALENTS

[0165] The representative examples that follow are intended to help illustrate the invention, and are not intended to, nor should they be construed to, limit the scope of the invention. Indeed, various modifications of the invention and many further embodiments thereof, in addition to those shown and described herein, will become apparent to those skilled in the art from the full contents of this document, including the examples which follow and the references to the scientific and patent literature cited herein. It should further be appreciated that the contents of those cited references are incorporated herein by reference to help illustrate the state of the art.

[0166] The following examples contain important additional information, exemplification and guidance that can be adapted to the practice of this invention in its various embodiments and the equivalents thereof.

EXEMPLIFICATION

[0167] The compounds of this invention and their preparation can be understood further by the examples that illustrate some of the processes by which these compounds are prepared or used. It will be appreciated, however, that these examples do not limit the invention. Variations of the invention, now known or further developed, are considered to fall within the scope of the present invention as described herein and as hereinafter claimed.

[0168] According to the present invention, any available techniques can be used to make or prepare the inventive compounds or compositions including them. For example, a variety of solution phase synthetic methods such as those discussed in detail below may be used. Alternatively or additionally, the inventive compounds may be prepared using any of a variety combinatorial techniques, parallel synthesis and/or solid phase synthetic methods known in the art.

[0169] It will be appreciated as described below, that a variety of inventive compounds can be synthesized according to the methods described herein. The starting materials and reagents used in preparing these compounds are either available from commercial suppliers such as Aldrich Chemical Company (Milwaukee, Wis.), Bachem (Torrance, Calif.), Sigma (St. Louis, Mo.), or are prepared by methods well known to a person of ordinary skill in the art following procedures described in such references as Fieser and Fieser 1991, “Reagents for Organic Synthesis”, vols 1-17, John Wiley and Sons, New York, N.Y., 1991; Rodd 1989 “Chemistry of Carbon Compounds”, vols. 1-5 and supps, Elsevier Science Publishers, 1989; “Organic Reactions”, vols 1-40, John Wiley and Sons, New York, N.Y., 1991; March 2001, “Advanced Organic Chemistry”, 5th ed. John Wiley and Sons, New York, N.Y.; and Larock 1989, “Comprehensive Organic Transformations”, VCH Publishers. These schemes are merely illustrative of some methods by which the compounds of this invention can be synthesized, and various modifications to these schemes can be made and will be suggested to a person of ordinary skill in the art having regard to this disclosure.

[0170] The starting materials, intermediates, and compounds of this invention may be isolated and purified using conventional techniques, including filtration, distillation, crystallization, chromatography, and the like. They may be characterized using conventional methods, including physical constants and spectral data.

[0171] 1) Exemplary Compounds

[0172] Certain exemplary compounds of the invention are listed below and are referred to by compound number as indicated. ER-# Structure 1 805600 (IC375)

2 805894 (IC400)

3 806006

4 805985 (IC403)

5 805984

6 806002

7 805969

8 805971

9 805996

10 805639 (IC397)

11 805985 (IC405)

12 806007

13 805976

14 805975

15 805999

16 806011

17 805970

18 805972

19 805997

20 806010

21 806014

22 806094

23 806095

24 806097

25 806107

26 806123

27 806136

28 806181

29 806221

30 806220

31 806224

32 806228

33 806276

34 806275

35 806274

36 806273

37 806286

38 806287

39 806311

40 806317

41 806320

42 806329

43 806333

45 806336

46 806355

47 806358

48 806359

49 806363

50 806362

51 806361

52 806368

53 806372

54 806373

55 806374

56 806375

57 806383

58 806393

59 806401

60 806402

61 806404

62 806417

63 806419

64 806420

65 806421

66 806432

67 806435

68 806437

69 806569

70 806609

71 806610

72 806644

73 806645

74 806646

75 806647

76 806653

77 806671

78 806781

79 806790

80 806796

81 806820

82 806839

83 806840

84 806841

85 806842

86 806843

87 806844

88 806860

89 806874

90 806875

91 806878

92 806899

93 806900

94 806901

95 806902

96 806903

97 806904

98 806905

99 806987

100 807014

101 807015

102 807139

103 807140

104 807183

105 807240

106 807313

107 807377

108 807392

109 807400

110 807401

111 807399

112 807447

113 807448

114 807449

115 807450

116 807451

117 807452

118 807453

119 807454

120 807457

121 807458

122 807459

123 807460

124 807462

125 807463

126 807464

127 807465

128 807466

129 807467

130 807469

131 807496

132 807497

133 807498

134 807505

135 807506

136 807528

137 807531

138 807532

139 807543

140 807544

141 807546

142 807548

143 807549

144 807550

145 807562

146 807571

147 807573

148 807584

149 807585

150 807586

151 807587

152 807636

153 807649

154 807660

155 807662

156 807663

157 807703

158 807704

159 807748

160 807749

161 807750

162 807751

163 807754

164 807758

165 807759

166 807762

167 807779

168 807787

169 807788

170 807789

171 807790

172 807794

173 807835

174 807836

175 807837

176 807862

177 807865

178 807876

179 807892

180 807920

181 807930

182 807931

183 807952

184 807956

185 807962

186 807976

187 807977

188 807978

189 807980

190 808009

191 808028

192 808036

193 808039

194 808040

195 808041

196 808069

197 808078

198 808079

199 808080

200 808081

201 808082

202 808083

203 808084

204 808085

205 808086

206 808101

207 808102

208 808103

209 808107

210 808128

211 808151

212 808152

213 808153

214 808160

215 808164

216 808247

217 808254

218 808255

219 808256

220 808257

221 808259

222 808260

223 808261

224 808262

225 808266

226 808268

227 808269

228 808281

229 808283

230 808284

231 808285

232 808286

233 808287

234 808288

235 808289

236 808290

237 808291

238 808310

239 808311

240 808312

241 808313

242 808319

243 808322

244 808346

245 808347

246 808355

247 808356

248 808361

249 808362

250 808363

251 808364

252 808365

253 808370

254 808371

255 808372

256 808385

257 808386

258 808387

259 808388

260 808469

261 808470

262 808473

263 808496

264 808497

265 808498

266 808499

267 808500

268 808501

269 808513

270 808514

271 808541

272 808542

273 808543

274 808544

275 808548

276 808571

277 808576

278 808600

278 808617

279 808620

280 808622

281 808623

282 808624

283 808627

284 808628

285 808629

286 808631

287 808635

288 808636

289 808637

290 808658

291 808660

292 808661

293 808663

294 808665

295 808672

296 808673

297 808675

298 808691

299 808692

300 808702

301 808703

302 808704

303 808705

304 808711

305 808712

306 808713

307 808714

308 808717

309 808719

310 808720

311 808833

312 808834

313 808835

314 808836

315 808849

316 808983

317 808984

318 809047

319 809187

320 809189

321 809190

322 809191

323 809192

324 809193

325 809196

326 809197

327 809198

328 809199

329 809200

330 809201

331 809202

332 809203

333 809204

334 809205

335 809206

336 809207

337 809208

338 809209

339 809210

340 809211

341 809212

342 809213

343 809214

344 809215

345 809216

346 809217

347 809218

348 809219

349 809220

350 809221

351 809222

352 809223

353 809224

354 809225

355 809226

356 809227

357 809228

358 809229

359 809230

360 809231

361 809232

362 809233

363 809234

364 809235

365 809236

366 809237

367 809238

368 809251

369 809252

370 IC261

371 IC375

372 IC380

373 IC395

374 IC396

375 IC400

376 IC401

377 IC402

378 IC403

379 IC404

380 IC415

381 IC416

[0173] Experimental Procedures:

[0174] As described above, the present invention provides novel deazapurines having formula (I) described above and in certain classes and subclasses herein. The synthesis of several exemplenary compounds is described in detail below. It will be appreciated that the methods as described herein can be applied to each of the compounds as disclosed herein and equivalents thereof. Additionally, certain reagents and starting materials are well known to those skilled in the art. Although the following examples describe certain exemplary compounds, it will be appreciated that the use of alternate starting materials will readily yield other analogues encompassed by the invention.

[0175] General Reaction Procedures:

[0176] Unless mentioned specifically, reaction mixtures were stirred using a magnetically driven stirrer bar. An inert atmosphere refers to either dry argon or dry nitrogen. Reactions were monitored either by thin layer chromatography, or by proton nuclear magnetic resonance, of a suitably worked up sample of the reaction mixture.

[0177] General Work Up Procedures:

[0178] Unless mentioned specifically, reaction mixtures were cooled to room temperature or below then quenched, when necessary, with either water or a saturated aqueous solution of ammonium chloride or sodium bicarbonate. Desired products were extracted by partitioning between water and a suitable water-immiscible solvent (e.g. ethyl acetate, dichloromethane, diethyl ether). The desired product containing extracts were washed appropriately with water followed by a saturated solution of brine. On occasions where the product containing extract was deemed to contain residual oxidants, the extract was washed with a 10% solution of sodium sulphite in saturated aqueous sodium bicarbonate solution, prior to the aforementioned washing procedure. On occasions where the product containing extract was deemed to contain residual acids, the extract was washed with saturated aqueous sodium bicarbonate solution, prior to the aforementioned washing procedure (except in those cases where the desired product itself had acidic character). On occasions where the product containing extract was deemed to contain residual bases, the extract was washed with 10% aqueous citric acid solution, prior to the aforementioned washing procedure (except in those cases where the desired product itself had basic character). Post washing, the desired product containing extracts were dried over anhydrous sodium or magnesium sulphate, then filtered. The crude products were then isolated by removal of solvent(s) by rotary evaporation under reduced pressure, at an appropriate temperature (generally less than 45° C.).

[0179] General Purification Procedures:

[0180] Unless mentioned specifically, chromatographic purification refers to flash column chromatography on silica gel, using a single solvent or mixed solvent as eluent. Suitably purified desired product containing elutes were combined and concentrated under reduced pressure at an appropriate temperature (generally less than 45° C.) to constant mass.

[0181] Experimentals for Certain Exemplary Compounds:

[0182] In certain embodiments, compounds 1 and 2 were prepared according to the procedure of Temple, C.; Smithy, B. H.; Montgomery, J. A.; J Org Chem. 1973, 38, 613-5.

[0183] Dry HCl (gas) was bubbled through a 2 M solution of nitrile (R₂—CN) in ethyl ether containing 1 mole equivalent of ethanol at −10° C. for 1-2 hours. After stirring from additional an hour to overnight at room temperature, nitrogen was bubbled through to purge excess HCl gas and ether. The remaining slurry or suspension was filtered, washed with ether three times and then dried under vacuum to give the corresponding ethyl imidate hydrogen chloride.

[0184] A mixture of 1 (1 mmol) and the ethyl imidate hydrogen chloride (1.1 mmol) in 5 mL of ethanol was heated at 65-70° C. until reaction was completed (1.5 h to overnight). The mixture was cooled to room temperature, diluted with 20 mL of water, stirred for 30 min., filtered and washed with water. The cake was collected and dried under vacuum to give the desired product 3.

[0185] A solution of 3 (1 mmol) in 2.8 mL of 57% HI (aq., 20 mmol) was heated at reflux until reaction was completed (12-20 h). The mixture was cooled to 0° C., slowly diluted with 5 N NaOH solution (19 mmol) and then with 1 mL of sat. NaHCO₃ to pH˜9. The resulting mixture was extracted with either ethyl acetate or ethyl acetate/THF mixture until extraction was completed. The combined extracts was dried over Na₂SO₄, filtered and concentrated to give the desired product 4 as free form. Washing the product with ethyl acetate resulted in a better purity if necessary in certain cases. The HI mono-salt form of 4 was obtained after cooling the reaction mixture to room temperature, filtration, washing with water and drying the collected yellow solid in high vacuumn.

[0186] A mixture of 1 (300 mg, 1.3 mmol) and tetraethyl orthocarbonate (2.6 mmol) in 10 mL of acetic acid was stirred at room temperature overnight and reaction was completed. The reaction mixture was concentrated under reduced vacuum and the residue was diluted with sat. NaHCO₃, extracted with EtOAc, dried over Na₂SO₄, filtered, concentrated to give a brownish solid. This solid was dissolved in 24 mL of H₂O-MeOH (1:1) solution containing 1.2 g of KOH and heated at reflux for 2.5 h. After cooling to room temperature, the mixture was extracted with EtOAc. The extracts was washed with water, dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatography (10% MeOH-EtOAc) to give 5 (45 mg, 16%).

[0187] A solution of 1 (203 mg, 0.88 mmol) in trifluoroacetic acid (2 mL) was heated at 70° C. for 12 h, cooled to room temperature, concentrated and the residue was diluted with sat. NaHCO₃ (10 ml) and EtOAc (10 mL). The separated aqueous phase was extracted with 4×10 mL of EtOAc and the combined organic layer was dried over Na₂SO₄, filtered and concentrated to give a yellow solid. This yellow solid was mixed with 3 mL of polyphosphoric acid, heated at 200° C. for 3 h and cooled to room temperature. The reaction mixture was carefully quenched with sat. NaHCO₃ (80 ml) and extracted with 4×20 mL of EtOAc. The combined organic layer was dried over Na₂SO₄, filtered and concentrated to give a brownish yellow solid. This solid was dissolved in 5 mL of 57% HI solution and heated at 110° C. for 12 h. After cooling to room temperature, the reaction mixture was carefully poured into sat. NaHCO₃ (60 ml) containing 3 mL of 1 N NaOH and extracted with 4×20 mL of EtOAc. The combined organic layer was dried over Na₂SO₄, filtered and concentrated and the product was purified by chromatography (50 to 100% EtOAc-hexanes) to give the desired product 6 (132 mg, 46% for 3 steps).

[0188] A mixture of methyl indole-5-carboxylate (27 g, 155 mmol) (or the corresponding 4-, 6- and 7-carboxylate), di-t-butyl dicarbonate (40 g, 1.2 eq.), Et₃N (26 mL, 1.2 eq.) and DMAP (0.1 g, 0.005 eq.) in THF (165 mL) was stirred at room temperature overnight. The reaction mixture was quenched by addition of sat. NaHCO₃ (350 mL). The separated aqueous layer was extracted once with EtOAc. The combined organic phase was concentrated and the product was purified by chromatography (5% and 10% EtOAc-hexanes) to provide 7 (42 g, 100%).

[0189] To a solution of 7 (42 g, 152 mmol) in dichloromethane (400 mL) at −78° C. was added a 1 M solution of DIBAL-H in toluene (460 mL, 3.0 eq.) during 30 min of period. The cooling bath was replaced with −40° C., the reaction mixture was stirred and warmed to −30° C. and TLC showed reaction was completed. The reaction was quenched with careful addition of MeOH (57 mL, 9.0 eq.) and water (19 mL, 9.0 eq.), diluted with EtOAc (150 mL) and then warmed to rt. The resulting suspension mixture was filtered through celite washing with EtOAc until the product was no longer detected. The filtrate was concentrated and the product was purified by chromatography (15% and 30% EtOAc-hexanes) to provide 8 (29 g, 75%).

[0190] Methanesulfonyl chloride (10.1 mL, 1.2 eq.) was added to a solution of 8 (27.0 g, 109 mmol, 1.0 eq.) and diisopropylethylamine (57 mL, 3.0 eq.) in dichloromethane (250 mL) at 0° C. during 5 min. After stirring additional 15 min. morpholine (14.3 mL, 1.5 eq. or cyclic or acyclic R′R″NH) was added to the reaction mixture and stirred at room temperature overnight. The mixture was poured into sat. NaHCO₃ (100 mL) and water (20 mL), the separated aqueous phase was extracted with 4×50 mL of EtOAc. The combined organic phase was dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatography (15% to 40% EtOAc-hexanes) to provide 9 (34.0 g, 99%).

[0191] Method A: To a solution of diisopropylamine (17.0 mL, 1.2 eq.) in THF (350 mL) at −78° C. was added nBuLi (2.5 M in hexanes, 48.6 mL, 1.2 eq.) over a 15 min period and the reaction mixture was stirred and warmed to room temperature after removing the cooling bath. The reaction mixture was cooled back to −78° C. and a solution of 9 (32 g, 101 mmol) in THF (120 mL) was introduced by cannulation during 15 min. The resulting mixture was stirred and warmed to −20° C. during 15 min and then Bu₃SnCl (31.5 mL, 1.15 eq.) was introduced. The mixture was stirred and warmed to room temperature and poured into a sat. NH₄Cl (300 mL). The separated aqueous phase was extracted with 3×100 mL of EtOAc. The combined organic phase was dried over Na₂SO₄, filtered, concentrated and the product was purified by vacuum chromatography (5% to 50% EtOAc-hexanes) to provide 10 (55 g, 89%).

[0192] Method B: This reaction was also carried out by following the same protocol as that used for the preparation of 15 from 14.

[0193] Compound 11 was prepared from indole-1-carboxylic acid tert-butyl ester in 86% following the same procedure for the preparation of 10 from 9.

[0194] Compound 12 was prepared from mono- or di-substituted indole following similar procedures for the preparation of 7 and 10.

[0195] A mixture of 4 (0.4 mmol, 1.0 eq., or 2 or 5 or 6), 10 (1.6 eq., or 11 or 12) and [(C₆H₅)₃P]₄Pd (0.1 eq.) in degassed DMF (1 mL) under nitrogen with or without K₂CO₃ (1.0 eq.) was heated at 110° C. for 18-28 h, cooled to room temperature and concentrated under high vacuum. The residue was diluted with sat. NaHCO₃ (10 mL) and EtOAc. The separated aqueous phase was extracted with EtOAc multiple times until there was no product detected. The combined organic phase was dried over Na₂SO₄, filtered and concentrated. The product was purified by chromatography (5% or 10% MeOH-EtOAc) to give the desired product 13. MS (ES) Compound # or/and (ER # or IC #) Structure of 13 ¹H NMR IC 400

¹H NMR 806014

287.3 (M − H)⁻ 806006

316.3 (M − H)⁻ 805985

278.3 (M + H)⁺ 805984

292.3 (M + H)⁺ 806002

306.3 (M + H)⁺ 805969

326.3 (M + H)⁺ 805971

354.3 (M + H)⁺ 805996

¹H NMR 805639 (IC 379)

¹H NMR 805895 (IC 405)

¹H NMR 806007

425.2 (M − H)⁻ 805976

¹H NMR 805975

¹H NMR 805999

¹H NMR 806011

393.3 (M + H)⁺ 805970

¹H NMR 805972

453.3 (M + H)⁺ 805997

469.2 (M − H)⁻ 806010

455.3 (M + H)⁺ 809189

¹H NMR 809190

¹H NMR 809191

¹H NMR 809192

¹H NMR 809193

¹H NMR

[0196]

[0197] To a mixture of 8 (5-hydroxymethyl-indole-1-carboxylic acid tert-butylester as an example, 24.4 g, 98.8 mmol), Et₃N (41 mL, 3 eq.) and DMAP (1.2 g, 0.1 eq.) in dichloromethane (185 mL) was added TBSCl (23.1 g, 1.5 eq.) at room temperature and the resulting mixture was stirred overnight. The reaction was quenched with the addition of sat. NaHCO₃ (200 mL) and the separated aqueous layer was extracted with 3×50 mL dichloromethane. The combined organic phase was dried over Na₂SO₄, filtered, concentrated and the product was purified by vacuum chromatography (3% EtOAc-hexanes) to provide 14 (5-tert-butyl-dimethyl-silanyloxymethyl)-indole-1-carboxylic acid tert-butyl ester) as a colorless oil (33.9 g, 95%).

[0198] To a solution of 14 (5-tert-butyl-dimethyl-silanyloxymethyl-indole-1-carboxylic acid tert-butyl ester as an example, 33.5 g, 92.7 mmol) in THF (650 mL) below −72° C. was added tBuLi (63 mL, 1.7 M in pentane, 1.2 eq.) dropwise over a period of 45 min and stirring was continued for an additional 40 min. The resulting brown solution was briefly warmed to −60° C. and then cooled back to below −72° C. Bu₃SnCl (31.6 mL, 1.3 eq.) was then introduced to the reaction mixture and stirred at 40° C. for 15 min. The reaction was quenched at −35° C. with sat. NaHCO₃ (250 mL) and the separated aqueous layer was extracted with 3×150 mL EtOAc. The combined organic phase was dried over Na₂SO₄, filtered, concentrated and the product was purified by vacuum chromatography (hexanes) to provide 15 (5-(tert-butyl-dimethyl-silanyloxymethyl)-2-tributylstannyl-indole-1-carboxylic acid tert-butyl ester) as a colorless oil (60.6 g, 100%).

[0199] A solution of 15 (5-(tert-butyl-dimethyl-silanyloxymethyl)-2-tributylstannyl-indole-1-carboxylic acid tert-butyl ester as an example, 60.6 g, 3.0 eq.) in DMF (100 mL) was added in four portions during 24 h period to a solution of 4 (R₂=Me, 8.51 g, 31.0 mmol), Pd(Ph₃P)₄ (3.2 g, 0.09 eq.) and Et₃N (26 mL, 3.0 eq.) in DMF (100 mL) with or without K₂CO₃ (1.0 eq.) at 110° C. under nitrogen atmosphere. The resulting mixture was stirred for 20 h, cooled to room temperature and concentrated. The residue was diluted with sat. NaHCO₃ (300 mL) and EtOAc (300 mL), filtered and washed with EtOAc to get rid of dark gray sludge. The separated aqueous phase from the filtrate was extracted with 6×200 mL EtOAc until no desired product detected by TLC. The combined organic phase was dried over Na₂SO₄, filtered and concentrated. The residue was diluted with EtOAc and the resulting suspension was filtered, washed with EtOAc and 2×MeOH to give 16 (4.27 g). The filtrate was concentrated and the residual product was purified by chromatography (0 to 5% MeOH-EtOAc) to give additional 16 (2.59 g). The products were combined to give 16 (7-[5-(tert-butyl-dimethyl-silanyloxymethyl)-1H-indol-2-yl]-2-methyl-3H-imidazo[4,5-b]pyridin-5-ylamine) as a greenish gray solid (6.86 g, 54%).

[0200] A solution of tBuOK in THF (1.66 M, 96.3 mL, 9.5 eq.) was added to a mixture of 16 (7-[5-(tert-butyl-dimethyl-silanyloxymethyl)-1 H-indol-2-yl]-2-methyl-3H-imidazo[4,5-b]pyridin-5-ylamine as an example, 6.86 g, 16.8 mmol) and di-tert-butyl dicarbonate (39 mL, 10 eq.) in THF (1.1 L) at below −28° C. during 40 min period. After stirring for 10 min, the reaction was quenched by addition of sat. NaHCO₃ (300 mL) and warmed to room temperature. The separated aqueous layer was extracted by 3×150 mL of EtOAc. The combined organic phase was dried over Na₂SO₄, filtered, concentrated and the product was purified by vacuum chromatography (10 to 20% EtOAc/hexanes) to provide a di-Boc-protected intermediate.

[0201] The di-Boc-protected intermediate was then dissolved in 55 mL THF containing Et₃N (55 mL), DIBOC (22.5 g, 6.0 eq.) and DMAP (0.21 g, 0.1 eq.) and heated at 65° C. for 5 h. After cooling to room temperature, the mixture was concentrated and the product was purified by vacuum chromatography (10% EtOAc-hexanes) to provide tetra-Boc-protected intermediate.

[0202] The tetra-Boc-protected intermediate was then dissolved in a solution of HF/pyridine in THF (0.89 M, 5.3 eq., HF/pyridine solution was prepared by mixing of 10 g of 70% HF/pyridine, 52.5 mL of pyridine and 330 mL of THF) and stirred at room temperature for 40 h. The reaction mixture was then carefully quenched with sat. NaHCO₃ (250 mL) and the separated aqueous layer was extracted by 3×50 mL of EtOAc. The combined organic phase was washed with brine (50 mL), dried over Na₂SO₄, filtered, concentrated and the product was purified by vacuum chromatography (10 to 50% EtOAc-hexanes) to provide 17 (5-di-(tert-butoxycarbonyl)amino-7-(1-tert-butoxycarbonyl-5-hydroxylmethyl-1H-indol-2-yl)-2-methyl-imidazo[4,5-b]pyridine-3-carboxylic acid tert-butyl ester, 5.64 g, 48% for three steps) as a light yellow solid.

[0203] Methylsulfonylchloride (0.14 mL, 1.5 eq.) was added to a mixture of 17 (5-di-(tert-butoxycarbonyl)amino-7-(1-tert-butoxycarbonyl-5-hydroxylmethyl-1H-indol-2-yl)-2-methyl-imidazo[4,5-b]pyridine-3-carboxylic acid tert-butyl ester as an example, 830 mg, 1.2 mmol) and diisopropylethylamine (2.08 mL, 10 eq.) in dichloromethane (10 mL) at 0° C. and the resulting mixture was stirred and warmed to room temperature. After stirring for 7 h at room temperature, the mixture was kept at 0° C. for two days, warmed to room temperature and concentrated to half of its volume. The product was then purified by chromatography (20% to 30% EtOAc/hexanes) to give 18 (5-di-(tert-butoxycarbonyl)amino-7-(1-tert-butoxycarbonyl-5-chloromethyl-1H-indol-2-yl)-2-methyl-imidazo[4,5-b]pyridine-3-carboxylic acid tert-butyl ester, 770 mg, 90%).

[0204] A mixture of 17 (5-di-(tert-butoxycarbonyl)amino-7-(1-tert-butoxycarbonyl-5-hydroxylmethyl-1H-indol-2-yl)-2-methyl-imidazo[4,5-b]pyridine-3-carboxylic acid tert-butyl ester as an example, 122 mg, 0.18 mmol) and Dess-Martin periodinane (223 mg, 3.0 eq.) in dichloromethane (4 mL) was stirred at room temperature for 1 h. The resulting mixture was diluted with diethyl ether (60 mL), stirred for 20 min and filtered through celite washing with diethyl ether. The filtrate was washed with sat. NaHCO₃ (20 mL) containing Na₂S₂O₃ (500 mg) and the aqueous phase was back extracted with 2×25 mL diethyl ether. The combined organic layer was dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatography (10 to 30% EtOAc-hexanes) to provide 19 (5-di-(tert-butoxycarbonyl)amino-7-(1-tert-butoxycarbonyl-5-formyl-1H-indol-2-yl)-2-methyl-imidazo[4,5-b]pyridine-3-carboxylic acid tert-butyl ester, 117 mg, 96%).

[0205] A solution of KMnO₄ (436 mg, 2 eq.) and KH₂PO₄ (563 mg, 3 eq.) in water (15 mL) was added to a solution of 19 (5-di-(tert-butoxycarbonyl)amino-7-(1-tert-butoxycarbonyl-5-formyl-1H-indol-2-yl)-2-methyl-imidazo[4,5-b]pyridine-3-carboxylic acid tert-butyl ester as an example, 958 mg, 1.38 mmol) in tBuOH (10 mL) at room temperature during 3 min and the resulting mixture was stirred for 30 min. The mixture was then diluted with EtOAc (20 mL), filtered through celite washing with EtOAc. The filtrate was diluted with brine (60 mL), water (40 mL) and EtOAc (200 mL). The separated aqueous phase was extracted with 3×30 mL of EtAOc. The combined organic layer was dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatography (30 to 100% EtOAc/hexanes) to provide 20 (2-(3-tert-butylcarbonyl-5-di-(tert-butylcarbonyl)amino-2-methyl-3H-imidazo[4,5-b]pyridin-7-yl)-indole-1,5-carboxylic acid 1-tert-butyl ester, 678 mg, 69%).

[0206] A mixture of (mono- or di-) substituted benzyl chloride (or bromide) or bromomethylnaphthalene or chloromethyl pyridine hydrochloride (20 mmol) and methylamine (22 mL, 40% in water, 10 eq.) in MeOH (18 mL) was stirred at room temperature for 1-5 days until reaction was completed. After concentration, the reaction mixture was diluted with sat. NaHCO₃ (50 mL), extracted with EtAOc until there was no product detected. The combine extracts were dried over Na₂SO₄, filtered, concentrated to give the product 21.

[0207] Amines 22-26 were prepared following a modified procedure disclosed in published PCT application number WO 01/00610 A1.

[0208] Methanesulfonyl chloride (0.80 mL, 1.2 eq.) was added to a solution of 2-(ethyl-phenyl-amino)-ethanol (1.43 g, 8.65 mmol) and diisopropylethylamine (3.0 mL, 2.0 eq.) in dichloromethane (10 mL) at 0° C. and the resulting mixture was stirred for 15 min. A solution of ammonia (20 mL, 2 M in MeOH) was then introduced and the resulting mixture was stirred at room temperature for five days and concentrated. The residue was diluted with a solution of HCl (7 mL, 1 N) and washed with 3×EtOAc. The aqueous phase was treated with a solution of NaOH (15 mL, 1 N) and extracted once with EtOAc. The extract was dried over Na₂SO₄, filtered, concentrated to give the product 27.

[0209] To a solution of 2-benzyloxy-propane-1,3-diol (5.0 g, 27.4 mmol) in 5:1 THF-DMF (200 mL) at 0° C. was added NaH (1.5 g, 2.3 eq.) followed by methyl iodide (5.1 mL, 3.0 eq.). The resulting white slurry mixture was stirred at room temperature over weekend. The reaction mixture was quenched with sat. NH₄Cl, extracted with EtOAc, dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatography (50% EtOAc/hexanes) to give (2-methoxy-1-methoxymethyl-2-ethoxymethyl)-benzene (5.6 g, 97%).

[0210] A mixture of (2-methoxy-1-methoxymethyl-2-ethoxymethyl)-benzene (5.5 g) and Pd(OH)₂ (0.4 g) in MeOH (150 mL) was stirred at room temperature under hydrogen gas until reaction was completed. The reaction mixture was filtered and concentrated to give 1,3-dimethoxy-propan-2-ol (3.0 g, 96%).

[0211] Methanesulfonyl chloride (0.61 mL, 2.0 eq.) was added to a solution of 1,3-dimethoxy-propan-2-ol (0.50 g, 4.14 mmol) and triethylamine (2.3 mL, 4.0 eq.) in dichloromethane (2 mL) at 0° C. and the resulting mixture was stirred for 15 min. The reaction was quenched by sat. NaHCO₃ and the mixture was extracted with EtOAc. The combined extracts were dried over Na₂SO₄, filtered and concentrated. The residue and NaN₃ (0.80 g, 3.0 eq.) was dissolved in DMSO (10 mL) and heated at 90° C. over weekend. After cooling to room temperature, the mixture was diluted with sat. NaHCO₃ and extracted with diethyl ether. The combined extracts were dried over Na₂SO₄, filtered and concentrated to give azide intermediate (320 mg, 48%).

[0212] A mixture of the azide intermediate (320 mg) and Pd(OH)₂ in MeOH (15 mL) was stirred at room temperature under hydrogen gas for 1 h. The reaction mixture was filtered and concentrated to give 28 (150 mg, 63%).

[0213] A mixture of ethyl-phenyl-amine (4.15 mL, 33 mmol), allyl bromide (4.3 mL, 1.5 eq.) and K₂CO₃ (9.1 g, 2.0 eq.) in acetone (50 mL) was heated at reflux for overnight. After cooling to room temperature, the reaction mixture was diluted with water (50 mL) and EtOAc (100 m). The separated organic phase was dried over Na₂SO₄, filtered and concentrated and the product was purified by chromatography (10% EtOAc/hexanes) to give allyl-ethyl-phenyl-amine (5.32 g, 100%).

[0214] A solution of OsO₄ (7.8 mL, 0.1 M in water, 0.03 eq.) was added to a mixture of allyl-ethyl-phenyl-amine (4.10 g, 25.3 mmol) and NMO (5.92 g, 2.0 eq.) in 9:1 acetone-water (40 mL) at room temperature and the resulting mixture was stirred overnight. The mixture was diluted with sat. NaHCO₃ (80 mL), sat. Na₂S₂O₃ (20 mL) and 1:1 Et₂O-hexanes (100 mL). The separated aqueous phase was extracted with 2×30 mL of EtOAc and the combined organic phase was dried over Na₂SO₄, filtered and concentrated and the product was purified by chromatography (30% EtOAc-hexanes) to give 3-(ethyl-phenyl-amino)-propane-1,2-diol (4.25 g, 86%).

[0215] Methanesulfonyl chloride (2.5 mL, 1.5 eq.) was added to a solution 3-(ethyl-phenyl-amino)-propane-1,2-diol (4.22 g, 21.6 mmol) and triethylaamine (9.03 mL, 3.0 eq.) in dichloromethane (20 mL) at −30 to −35° C. and the resulting mixture was stirred and warmed to 0° C. The reaction was quenched by sat. NaHCO₃ (30 mL) and the separated aqueous phase was extracted with 2×20 mL CH₂Cl₂ and 20 mL EtOAc. The combined extracts were dried over Na₂SO₄, filtered and concentrated. The residue was dissolved in MeOH (30 mL) and treated with NaOMe (2.3 g, 2.0 eq.) at 65-70° C. for 3 h. After cooling to room temperature, the mixture was diluted with sat. NaHCO₃ (50 mL) and extracted with 3×30 mL of EtOAc. The combined extracts were dried over Na₂SO₄, filtered and concentrated and the product was purified by chromatography (10% EtOAc/hexanes) to give ethyl-oxiranylmethyl-phenyl-amine (1.72 g, 45%).

[0216] A solution of ethyl-oxiranylmethyl-phenyl-amine (1.72 g, 9.65 mmol) and NaOMe (1.04 g, 2.0 eq.) in MeOH (8 mL) was heated at reflux for over weekend. After cooling to room temperature, the mixture was diluted with sat. NaHCO₃ (20 mL) and extracted with 3×20 mL of EtOAc. The combined extracts were dried over Na₂SO₄, filtered and concentrated and the product was purified by chromatography (30% EtOAc-hexanes) to give 1-(ethyl-phenyl-amino)-3-methoxy-propan-2-ol (1.95 g, 97%).

[0217] A solution of 1-(ethyl-phenyl-amino)-3-methoxy-propan-2-ol (1.95 g, 9.32 mmol) and NMO (2.18 g, 2.0 eq.) in dichloromethane (15 mL) was treated with TPAP (150 mg, 0.05 eq.) at room temperature until reaction was completed. The reaction mixture was diluted with sat. NaHCO₃ (50 mL) and extracted with 3×30 mL EtOAc. The combined extracts were dried over Na₂SO₄, filtered and concentrated and the product was purified by chromatography (10 to 15% EtOAc-hexanes) to give 1-(ethyl-phenyl-amino)-3-methoxy-propan-2-one (0.98 mg, 51%).

[0218] A mixture of 1-(ethyl-phenyl-amino)-3-methoxy-propan-2-one (17 mg, 0.08 mmol), hydroxylamine hydrochloride (30 mg) and pyridine (0.3 mL) in MeOH (0.4 mL) was stirred at room temperature for 1.5 h. The reaction mixture was diluted with sat. NaHCO₃ and extracted with 3×EtOAc. The combined extracts were dried over Na₂SO₄, filtered and concentrated. The residue was dissolved in THF (0.8 mL) and treated with lithium aluminum hydride (0.3 mL, 1 M in THF) at room temperature for overnight. Work-up and purification by chromatography (5:95 ratio of 2 M NH₃ in MeOH:CH₂Cl₂) gave 29 as light yellow oil.

[0219] Compound 30 was prepared from 3-phenoxy-propane-1,2-diol in 21% overall yield following the same procedures for the preparation of 29 from 3-(ethyl-phenyl-amino)-propane-1,2-diol.

[0220] A mixture of 3-(bromo-propyl)-benzene or bromomethyl-cyclohexane (1 M, 1.0 eq.) in MeOH and 40% MeNH₂ in water (60 eq.) was stirred at room temperature or at 45° C. until reaction was completed. After cooling to room temperature, the mixture was concentrated and the residue was diluted with saturated NaHCO₃ and extracted with 3×CH₂Cl₂ (or/and 3×EtOAc). The combined extracts were dried over Na₂SO₄, filtered and concentrated to give 31 or 32.

[0221] Methanesulfonylchloride (0.8 mL, 1.0 eq.) was added to a mixture of cyclopentyl-methanol (1.1 mL, 1.0 eq.) and ethyldiiospropylamine (3.9 mL, 10 eq.) in CH₂Cl₂ (5 mL) at 0° C. and the resulting mixture was stirred and warmed to room temperature. After addition of saturated NaHCO₃, the separated aqueous phase was extracted with CH₂Cl₂ and the combined organic layer was concentrated to give crude mesylate intermediate. This mesylate was then treated with MeNH₂ following the same procedure for the preparation of 31/32 to give 33.

[0222] A solution of TiCl₄ in CH₂Cl₂ (1 M, 1.56 mmol) was added to a mixture of 1,2-diphenyl-ethanone (307 mg, 1.56 mmol), Et₃N (655 μL) and methylamine (1.02 mL) in THF (5 mL) at 0° C. After stirring 1.5 h, a solution of NaBH₄ (280 mg, 37.8 mmol) in MeOH (8 mL) was added and the resulting mixture was stirred for 2 h. A saturated Na₂CO₃ was then added and the reaction mixture was stored in freezer overnight. After thawing, the organic layer was removed and the aqueous phase was extracted with 3×CH₂Cl₂. The combined organic phases were dried over Na₂SO₄, filtered and concentrated. Purification by preparative thin layer chromatography (80% EtOAc/hexanes) afforded 34 (195 mg, 59%).

[0223] Compounds 35 and 36 were prepared in a similar manner from 2-methoxy-1-phenyl-ethanone and cycloheptanone, respectively.

[0224] To a solution of Boc-nortropinone (0.5 g, 2.2 mmol, 1.0 equiv) in CH₂Cl₂ (10 mL) was added TFA (10 mL). The reaction mixture was stirred for 2 hours and then was concentrated. After addition of EtOAc and saturated NaHCO₃, the reaction mixture was extracted with 3×EtOAc. The combined organic layers were dried over Na₂SO₄, filtered and concentrated to give 37 (0.25 g).

[0225] To a solution of 2,5-dihydro-pyrrole-1-carboxylic acid phenyl ester (2 g, 10 mmol, 1.0 eq.) in Acetone/water (9:1, 20 mL) was added OsO₄ (4% in water, 1 mL) and NMO (2.3 g, 20 mmol, 2 eq.). The mixture was stirred at room temperature overnight, concentrated to remove most of the Acetone, poured into saturated NaHCO₃ and extracted with 3×EtOAc. The combined organic layers were dried over Na₂SO₄, filtered and concentrated. The crude mixture was purified by silica chromatography (70% to 90% EtOAc-Hexanes) to give 3,4-dihydroxy-pyrrolidine-1-carboxylic acid phenyl ester (2.04 g, 88%).

[0226] To a solution of 3,4-dihydroxy-pyrrolidine-1-carboxylic acid phenyl ester (1.93 g, 8.1 mmol, 1.0 eq.) in MeOH (20 mL) was added Palladium hydroxide and placed under H₂ for 4 h. The catalyst was filtered off through celite and rinsed with MeOH. The filtrate was concentrated (25° C.) to give 38 as reddish oil (840 mg, 100%).

[0227] To a suspension of NaH (8.99 g, 0.225 mol, 4.6 eq.) in DME (70 mL) at 0° C. was slowly added a solution of 1,4-dioxa-spiro[4.5]decan-8-one (7.56 g, 0.048 mol, 1.0 eq.) in DME (24 mL). After stirring for 30 minutes, a solution of MeI (14 mL, 0.225 mol, 4.6 eq.) in DME (70 ml) was slowly introduced over 7 h and the resulting mixture was lowly warmed to room temperature and stirred overnight. The reaction was quenched by slow addition of water until no more bubbling observed. The reaction mixture was poured over iced water and extracted with 3× hexanes. The organic layers were combined, dried over MgSO₄, filtered and concentrated. The crude mixture was purified by chromatography (100% hexanes to remove oil, then 5:1 Hexanes-EtOAc) to give 7,7,9,9-tetramethyl-1,4-dioxa-spiro[4.5]decan-8-one (4.16 g, 40%).

[0228] To a solution of 7,7,9,9-tetramethyl-1,4-dioxa-spiro[4.5]decan-8-one (4.15 g, 0.019 mol, 1,0 eq.) in THF (60 mL) was added 1 N HCl (30 mL) and the resulting mixture was stirred at room temperature overnight, concentrated to remove most of the THF, extracted with 3×EtOAc. The organic layers were combined, dried over MgSO₄, filtered and concentrated to give 2,2,6,6-tetramethyl-cyclohexane-1,4-dione as a white solid (3.43 g, >100%).

[0229] To a solution of 2,2,6,6-tetramethyl-cyclohexane-1,4-dione (0.40 g, 2.4 mmol, 1.0 eq.) in THF (8 mL) was added molecular sieves (4 Å, 80 mg), 2 M solution of MeNH₂ in THF (1.3 mL, 2.6 mmol, 1.1 eq.), and AcOH (0.17 mL, 3.0 mmol, 1,2 eq.). After 5 minutes of stirring, NaBH(OAc)₃ (0.71 g, 3.33 mmol, 1.4 eq.) was added and the resulting mixture was stirred at room temperature overnight. The reaction was quenched with the addition of saturated NaHCO₃. The mixture was then concentrated and the aqueous layer was extracted with 3×EtOAc. The combined organic layers were washed once with saturated NaHCO₃, dried over MgSO₄, filtered and concentrated to give a crude pale yellow oil that was crystallized to give 39 as a white crystals (0.40 g, >100%).

[0230] To solution of methyltriphenylphosphonium bromide (17 g, 1.5 eq.) in THF (100 mL) at 0° C. was added dropwise n-butyllithium (2.5 M in hexanes, 18 mL, 1.4 eq.) and the resulting mixture was stirred for 1 h. A solution of 1,4-dioxa-spiro[4.5]decan-8-one (5.0 g, 32 mmol, 1.0 eq.) in THF (10 mL) was then introduced dropwise and the resulting mixture was warmed to room temperature and stirred overnight. The reaction was quenched by addition of sat. NaHCO₃ and the separated aqueous layer was extracted with 4×EtOAc. The combined organic phase was dried over Na₂SO₄, filtered and concentrated. The residue was purified by chromatography (5% to 10% EtOAc/hexanes) to give 8-methyene-1,4-dioxa-spiro[4.5]decane (3.92 g, 79%).

[0231] To a solution of 8-methyene-1,4-dioxa-spiro[4.5]decane (2.0 g, 13 mmol, 1.0 eq.) in THF (10 mL) at 0° C. was added dropwise 9-BBN (0.5 M in THF, 104 mL, 4.0 eq.) and the resulting mixture was stirred for 15 min and then warmed to room temperature and stirred overnight. Then NaBO₄ 4H₂O (32 g, 16 eq.) was introduced at 0° C. portionwise and the resulting mixture was warmed to room temperature and stirred overnight, diluted with hexanes (30 mL) and the separated aqueous phase was extracted with EtOAc. The combined organic phase was dried over over Na₂SO₄, filtered and concentrated. The residue was purified by silica gel chromatography (50% to 100% EtOAc-hexanes) to give (1,4-dioxa-spiro[4.5]dec-8-yl)-methanol (1.5 g, 67%).

[0232] To a solution of (1,4-dioxa-spiro[4.5]dec-8-yl)-methanol (1.0 g, 5.8 mmol, 1.0 eq.) and ethyldiisopropylamine (17 mL, 3.0 eq.) in methylene chloride (4 mL) at 0° C. was added dropwise MsCl (0.46 mL, 1.0 eq.) and the resulting mixture was warmed to room temperature and stirred for 2 h. The reaction was quenched by addition of sat. NaHCO₃ and the separated aqueous phase was extracted with 3× methylene chloride and 4×EtOAc. The combined organic phase was dried over over Na₂SO₄, filtered and concentrated to give a crude methanesulfonic acid 1,4-dioxa-spiro[4.5]dec-8-ylmethyl ester.

[0233] A mixture of the crude methanesulfonic acid 1,4-dioxa-spiro[4.5]dec-8-ylmethyl ester (400 mg) in MeOH (2 mL) and aqueous MeNH₂ (40% w/w, 5 mL) was heated at reflux (60° C. oil both) for overnight. The reaction was quenched by addition of sat. NaHCO₃ and the separated aqueous phase was extracted with 4× methylene chloride and 4×EtOAc. The combined organic phase was dried over over Na₂SO₄, filtered and concentrated to give crude 40 as brown oil.

[0234] To a solution of 4-oxo-piperidine-1-carboxylic acid benzyl ester (0.50 g, 2.14 mmol, 1.0 eq.) in THF (20 mL) was added dibromodifluoromethane (0.90 mL, 4.5 eq.) at −30° C. followed by HMPA (1.75 mL, 4.5 eq.). The cooling bath was removed and the reaction mixture was swirled periodically. After 30 min, zinc dust (0.63 g, 4.5 eq.) and HMPA (80 μL 0.4 eq.) was added and the mixture was heated at reflux for 18 h. Upon cooling to room temperature, the residue was washed with diethyl ether several times. The combined ether washings were washed successively with saturated aqueous copper (II) sulphate, brine, dried over Na₂SO₄ and concentrated. The residue was purification by chromatography (20% EtOAc-hexanes) to afford 4-difluoromethylene-piperidine-1-carboxylic acid benzyl ester (0.32 g, 56%) as a colorless oil.

[0235] A mixture of 4-difluoromethylene-piperidine-1-carboxylic acid benzyl ester (269 mg) and Pearlman's catalyst in methanol (2.5 mL) was stirred under hydrogen atmosphere (using hydrogen filled balloon) for 4 h at room temperature. The reaction mixture was filtered through celite and the filtrate was concentrated to give 41 (138 mg) as pale yellow oil.

[0236] Following the same procedure to prepare 41, 4-difluoromethylene-piperidine-1-carboxylic acid 2,2-dimethyl-propyl ester (368 mg) was prepared using 4-oxo-piperidine-1-carboxylic acid 2,2-dimethyl-propyl ester (500 mg). The 4-difluoromethylene-piperidine-1-carboxylic acid 2,2-dimethyl-propyl ester (368 mg) in methylene chloride (1.0 mL) at room temperature was treated with trifluoroacetic acid (TFA, 0.5 mL) for 1.5 h. After concentration of of the reaction mixture, the crude 42 was used directly without further purification.

[0237] To a solution of 2-amino-cyclohexanol (3.50 g, 23.0 mmol, 1.0 eq.) in CH₂Cl₂ (100 mL) was added ethylchloroformate (2.65 mL, 1.2 eq.) followed by an aqueous solution of K₂CO₃ (16.0 g in 200 mL of H₂O). The mixture was stirred vigorously for 1 h. The separated aqueous layer was extracted twice with CH₂Cl₂. The combined organic layers were dried over MgSO₄, filtered and concentrated to give (2-hydroxy-cyclohexyl)-carbamic acid ethyl ester (4.36 g, >100%).

[0238] To a solution of (2-hydroxy-cyclohexyl)-carbamic acid ethyl ester (2.06 g, 11.0 mmol, 1.0 eq.) in THF (80 mL) was added LiAlH₄ (1.09 g, 28.7 mmol, 2.6 eq.) and the resulting mixture was heated at 65° C. for 2 h. The reaction mixture was cooled to 0° C., quenched with water, and the separated aqueous phase was extracted with 3×EtOAc. The combined organic phase was dried over MgSO₄, filtered and concentrated to give 2-methylamino-cyclohexanol (1.19 g, 84%).

[0239] To a solution of 2-methylamino-cyclohexanol (0.204 g, 1.58 mmol, 1.0 eq.) and di-tert-butyl dicarbonate (0.422 g, 1.2 eq.) in CH₂Cl₂ (7.0 mL) was added was added a solution of K₂CO₃ in water (1.09 g in 14.0 mL of H₂O) and the resulting mixture was stirred vigorously for 1 h. The separated aqueous layer was extracted twice with CH₂Cl₂. The combined organic phase was dried over MgSO₄, filtered and concentrated to give (2-hydroxy-cyclohexyl)-methyl-carbamic acid tert-butyl ester (0.332 g, 92%).

[0240] To a solution of (2-hydroxy-cyclohexyl)-methyl-carbamic acid tert-butyl ester (0.237 g, 1.03 mmol, 1.0 eq.) in CH₂Cl₂ (7.0 mL) at 0° C. was added molecular sieves (4 Å, 3 mL). The reaction was stirred for 5 minutes and then NMO (0.422 g, 3.5 eq.) and TPAP (0.025 g, 0.07 eq.) were introduced. The reaction mixture was stirred at 0° C. for 5 minutes, and then 40 minutes at room temperature. After diluted with hexanes, the reaction mixture was passed through a silica gel pad, using hexanes at the beginning to remove CH₂Cl₂, and then using a 1:1 mixture of hexanes-EtOAc to get the desired product. After concentration of the hexanes-EtOAc filtrate, methyl-(2-oxo-cyclohexyl)-carbamic acid tert-butyl ester was obtained as a white solid (0.235 g, 100%).

[0241] To a solution of methyl-(2-oxo-cyclohexyl)-carbamic acid tert-butyl ester (0.202 g, 0.89 mmol, 1.0 eq.) in CH₂Cl₂ (3.0 mL) was added TFA (1.0 mL) and the reaction mixture was stirred at room temperature for 3 h. The reaction mixture was then concentrated to give 43 (0.285 g, >100%).

[0242] To a solution of cyclopentylamine (5.8 mL, 59 mmol, 1.0 eq.) in CH₂Cl₂ (250 mL) at room temperature was added ethylchloroformate (7.3 mL, 1.3 eq.) followed by an aqueous solution of K₂CO₃ (37 g in 500 mL of H₂O). The mixture was stirred vigorously for 1 h. The separated aqueous layer was extracted twice with CH₂Cl₂. The combined organic layers were dried over MgSO₄, filtered and concentrated to give cyclopentyl-carbamic acid ethyl ester (9.6 g, 88%).

[0243] To a solution of the cyclopentyl-carbamic acid ethyl ester (6.00 g, 32.4 mmol, 1.0 eq.) in THF (250 mL) was added LiAlH₄ (3.08 g, 2.5 eq.) and the resulting mixture was heated at 65° C. for 2 h. The reaction was then cooled to 0° C. and quenched by addition of water. The separated aqueous layer was extracted with 3×EtOAc. The combined organic phase was dried over MgSO₄, filtered and concentrated to give 44 (2.01 g, 62%).

[0244] Compounds 45-58 were prepared following the same procedures for the preparation of 44 from the corresponding primary amines.

[0245] To a solution of cyclopentanone (25.0 mL, 0.28 mol, 1.0 eq.) in toluene (100 mL), was added pyrrolidine (27.5 mL, 1.2 eq.). The reaction was equipped with a Dean-Stark and heated at reflux overnight. The reaction mixture was cooled to room temperature and concentrated to give the crude 1-cyclopent-1-enyl-pyrrolidine (45.8 g, >100%).

[0246] To a solution of Pd(OAc)₂ (0.06 g, 0.06 eq.), PPh₃ (0.32 g, 0.24 eq.) and carbonic acid 2-ethoxycarbonyloxymethyl-allyl ester ethyl ester (1.23 g, 5.30 mmol, 1.0 eq., prepared following Tetrahedron 1998, 54(49), 14885-14904 ) in CH₃CN (30 ml) was added 1-cyclopent-1-enyl-pyrrolidine (1.01 g, 1.4 eq.) and the resulting mixture was heated at 45° C. for 35 minutes. Then water (15 mL) was introduced and the reaction mixture was heated at 50° C. for 1 h, cooled to room temperature and diluted with EtOAc (30 mL). The separated aqueous phase was extracted twice with EtOAc. The combined organic phase was dried over MgSO₄, filtered and concentrated. The residue was purified by silica gel chromatography (10% to 15% EtOAc-hexanes) to give 3-methylene-bicyclo[3,2,1]octan-8-one (0.14 g, 70%) as a pale yellow liquid.

[0247] To a solution of 3-methylene bicyclo[3,2,1]octan-8-one (0.14 g, 1.04 mmol, 1.0 eq.) in benzene (10 mL) was added ethylene glycol (0.65 g, 16 eq.) and PTSA (0.01 g, 0.06 eq.). The reaction was equipped with a Dean-Stark and heated at reflux overnight. After cooling to room temperature, Et₃N (0.15 mL) was introduced and the resulting mixture was passed through a cake of SiO₂ and MgSO₄. The cake was washed with CH₂Cl₂ and the combined filtrates were concentrated to give 3-methylene bicyclo[3,2,1]octan-8-one ethylene ketal (0.21 g, >100%).

[0248] To a solution of 3-methylenyl bicyclo[3,2,1]octan-8-one ethylene ketal (0.21 g, 1.15 mmol, 1.0 eq.) in CH₂Cl₂ (2 mL) at −78° C. was bubbled O₃ until the reaction stayed blue (about 3 min). The O₃ bubbling was stopped and the reaction mixture was stirred for 5 min at −78° C. The reaction was quenched by addition of triphenylphosphine (0.43 g, 1.4 eq.) and stirring at −78° C. for 10 minutes. The reaction mixture was allowed to warm at room temperature, stirred for 40 minutes and concentrated. The residue was purified by silica gel chromatography (10% to 15% EtOAc-hexanes) to give bicyclo[3,2,1]octane-3,8-dione 8-ethylene ketal as a colorless oil (0.08 g, 40%).

[0249] To a solution of bicyclo[3,2,1]octane-3,8-dione8-ethylene ketal (53.1 mg, 0.27 mmol, 1.0 eq.) in THF (1.0 mL) at 0° C. was added Et₃N (0.11 mL, 2.9 eq.) followed by MeNH₂ (2.0 M in THF, 0.21 mL, 1.5 eq.). After stirring at room temperature for 5 minutes, TiCl₄ (0.30 mL, 10.0 eq.) was introduced dropwise and the resulting mixture was stirred at 0° C. for 45 minutes. A solution of NaBH₄ (53.1 mg, 5.1 eq.) in MeOH (2.0 mL) was then introduced and the resulting mixture was stirred at 0° C. for 1 h. The reaction was quenched with saturated NaHCO₃ and the separated aqueous layer was extracted with 3×EtOAc. The combined organic phase was dried over MgSO₄, filtered and concentrated to give the crude product, 3-methylamino-bicyclo[3,2,1]octan-8-one ethylene ketal (24.1 mg).

[0250] To a solution of 3-methylamino-bicyclo[3,2,1]octan-8-one ethylene ketal (94.5, 0.48 mmol, 1.0 eq.) in acetone (2.0 mL) was added 1N HCl (1.5 mL) and the reaction was stirred overnight at room temperature. The reaction mixture was neutralized with saturated NaHCO₃ until pH was higher than 7, extracted with 3×EtOAc. The combined organic phase was dried over MgSO₄, filtered and concentrated to give 49 (40.0 mg, 54%).

[0251] To a solution of (3,3-dimethyl-1,5-dioxa-spiro[5,5]undec-9-yl)-methyl-amine hydrochloride (1.0 g, 4 mmol, 1.0 eq.) in THF (12 mL) was added di-tert-butyl dicarbonate (1.1 mL, 1.2 eq.), triethylamine (2 mL) and DMAP (catalytical amount). The resulting mixture was heated at 90° C. for 6, cooled to room temperature, poured in saturated NaHCO₃, and the separated aqueous layer was extracted with 3×EtOAc. The combined organic layers were dried over Na₂SO₄, filtered and concentrated. The residue was purified by silica gel chromatography (10% EtOAc/hexanes) to give (3,3-dimethyl-1,5-dioxa-spiro[5,5]undec-9-yl)-methyl-carbamic acid tert-butyl ester (1.4 g, 91%) as a white solid.

[0252] To a solution of (3,3-dimethyl-1,5-dioxa-spiro[5,5]undec-9-yl)-methyl-carbamic acid tert-butyl ester (1.27 g, 3.63 mmol, 1.0 eq.) in acetone (40 mL) and water (20 mL) was added PPTS (228 mg, 0.25 eq.) and the resulting reaction was heated to reflux overnight, cooled to room temperature, concentrated to 20 mL, poured in saturated NaHCO₃ and extracted with 3×EtOAc. The combined organic layers were dried over Na₂SO₄, filtered and concentrated. The residue was purified by silica gel chromatography (hexanes to 20% EtOAc/hexanes) to give methyl-(4-oxo-cyclohexyl)-carbamic acid tert-butyl ester (735 mg, 88%) as a white solid.

[0253] To a solution of methyl-(4-oxo-cyclohexyl)-carbamic acid tert-butyl ester (0.69 g, 3.04 mmol, 1.0 eq.) in THF (25 mL) at −30° C. was added CBr₂F₂ (1.25 mL, 4.5 eq.) follow slow addition of by P(N(CH₃)₂)₃. The resulting mixture was warmed to room temperature over 0.5 h and Zn was introduced. The resulting mixture was stirred at reflux for 16 h, cooled to room temperature and diluted with Et₂O. The organic phase was decanted and the aqueous phase extracted with 2×Et₂O. The combined organic phase was washed with saturated CuSO₄ solution until it stayed blue, dried over Na₂SO₄, filtered and concentrated. The residue was purified by chromatography (20% EtOAc-Hexanes) to give (4-difluoromethylene-cyclohexyl)-methyl-carbamic acid tert-butyl ester (475 mg, 60%) as a white solid.

[0254] To a solution of (4-difluoromethylene-cyclohexyl)-methyl-carbamic acid tert-butyl ester (150 mg, 0.57 mmol, 1.0 eq.) in CH₂Cl₂ (1.5 mL) was added TFA (1.5 mL). The reaction mixture was stirred for 4 h and then was concentrated to give 50 (85 mg). The crude compound was taken to the next step without further purification.

[0255] To a solution of cyclopropylamine (5.0 g, 87.5 mmol) and triethylamine (30 mL) in dichloromethane (100 mL) at 0° C. was added dropwise benzyl chloroformate (15.0 mL, 10.5 mmol) and the resulting mixture was stirred for 2 h. Additional benzyl chloroformate (1 mL) was added and the resulting reaction mixture was stirred overnight. The reaction was then quenched by addition of a saturated NaHCO₃ and the separated aqueous phase was extracted several times with dichloromethane. The combined dichloromethane extracts were dried over Na₂SO₄, filtered and concentrated. The residue was purified by chromatography (15% EtOAc to 5% MeOH/EtOAc) to give cyclopropyl-carbamic acid benzyl ester (11.8 g, 71%).

[0256] To a solution of cyclopropyl-carbamic acid benzyl ester (11.8 g) and methyl iodide (excess) in THF (80 mL) and DMF (20 mL) at 0° C. was added NaH (2.20 g, 91.6 mmol) and the resulting mixture was warmed to room temperature and stirred overnight. The reaction was then quenched at 0° C. by sat. NaHCO₃. The separated aqueous phase was extracted several times with EtOAc. The combined extracts were dried over Na₂SO₄, filtered and concentrated. The residue was purified by chromatography (5% to 20% EtOAc/hexanes) to give cyclopropyl-methyl-carbamic acid benzyl ester (11.32 g, 91%).

[0257] A mixture of cyclopropyl-methyl-carbamic acid benzyl ester (10.7 g) and Pd(OH)₂ in MeOH (100 mL) was stirred at room temperature under H₂ balloon for 17 h, diluted with concentrated HCl (4.8 mL), filtered through celite and concentrated. The residue was azeotroped with toluene several times to give cyclopropyl-methyl-amine hydrochloride (51, 5.75 g). The crude material was used without further purification.

[0258] To a solution of (tetrahydro-furan-3-yl)-methanol (1.00 g, 9.79 mmol, 1.0 eq.), PPh₃ (3.85 g, 1.5 eq.) and imidazole (1.33 g, 2.0 eq.) in CH₂Cl₂ (15 mL) at 0° C. was added I₂ (3.73 g, 1.5 eq.) and the resulting mixture was stirred at 0° C. for 30 min and then at room temperature for 30 min. The reaction mixture was diluted with sat. Na₂S₂O₃ solution and the separated aqueous layer was extracted by 3×EtOAc and 4×CH₂Cl₂. The combined extracts were dried over Na₂SO₄, filtered and concentrated. The residue was purified by chromatography (15% EtOAc/hexanes) to give 3-iodomethyl-tetrahydro-furan as yellow oil (1.59 g, 76%).

[0259] A mixture of 3-iodomethyl-tetrahydro-furan (500 mg, 2.36 mmol, 1.0 eq.) and MeNH₂ (40% in H₂O, 1.62 mL, 8.0 eq.) in MeOH (1 mL) was heated at 60° C. for 3 h. After cooling to room temperature, the reaction mixture was diluted with excess Et₃N and concentrated. This process was repeated until no MeNH₂ was detected by ¹HNMR₁ The residual yellow oil (52) was used directly without further purification.

[0260] To a solution of 1-methoxymethyl-propylamine (2.50 g, 24.3 mmol, 1.0 eq.) in dioxane (15 mL) was added an aqueous solution of K₂CO₃ (15 g in 15 mL of H₂O) and the mixture was cooled to 0° C. CBZ-Cl (4.16 mL, 1.2 eq.) was then introduced and the resulting mixture was warmed to room temperature and stirred for 3 h, extracted with EtOAc. The combined organicphase was dried over Na₂SO₄, filtered and concentrated. The residue was purified by chromatography (hexanes to 40% EtOAc/hexanes) to give (1-methoxymethyl-propyl)-carbamic acid benzyl ester (4.4 g, 76%) as a white solid.

[0261] To a solution of (1-methoxymethyl-propyl)-carbamic acid benzyl ester (4.4 g, 18.5 mmol, 1.0 eq.) and MeI (6.9 mL, 111 mmol, 6 eq.) in THF/DMF (4:1, 50 mL) at 0° C. was slowly added NaH (1.35 g, 55.5 mmol, 3 eq.). The resulting mixture was warmed to room temperature and stirred over night. The reaction was quenched carefully by slow addition of water until no bubbling (H₂) was observed. The reaction mixture was poured over ice water and extracted with 3×EtOAc. The combined organic phase was dried over Na₂SO₄, filtered and concentrated. The residue was purified by silica gel chromatography (30% to 50% EtOAc-hexanes) to give (1-methoxymethyl-propyl)-methyl-carbamic acid benzyl ester (4.4 g, 94%).

[0262] To a solution of (1-methoxymethyl-propyl)-methyl-carbamic acid benzyl ester (4.4 g, 17.5 mmol, 1.0 eq.) in MeOH (30 mL) was added Palladium hydroxide and the resulting mixture was stirred at room temperature under H₂ for 1.5 h. The mixture was then filtered through celite and washed with MeOH. The filtrate was treated with concentrated HCl (1.6 mL, 1 eq.) and concentrated to give 53 (2.67 g, 100%). ¹H NMR confirmed the compound. The crude compound was used to the next step without further purification.

[0263] Compound 54 was prepared from (1-benzyl-2-hydroxy-ethyl)-carbamic acid benzyl ester following the same procedures of step 2 and 3 for the parparation of 53.

[0264] (1-cyclohexylmethyl-2-hydroxy-ethyl)-methyl-carbamic acid benzyl ester was prepared from (1-cyclohexylmethyl-2-hydroxy-ethyl)-carbamic acid benzyl ester following the same procedure of step 2 for the preparation of 53. (1-Cyclohexylmethyl-2-hydroxy-ethyl)-methyl-carbamic acid benzyl ester was then treated with TFA-CH₂Cl₂ (1:1) at room temperature for 4 h. The mixture was then concentrated to give 55.

[0265] To a solution of (R)-(−)-leucinol (2.0 g, 17 mmol, 1.0 eq.), Et₃N (3.6 mL, 1.5 eq.) and DMAP (10 mg) in THF (2 mL) was added Boc₂O (4.5 g, 1.2 eq.) at room temperature. After stirring for 5 h, the reaction was quenched by water and the separated aqueous phase was extracted with 4× ether. The combined organic phase was dried over Na₂SO₄, filtered and concentrated. The residue was purified by chromatography (20% to 30% EtOAc/hexanes) to give (1-hydroxymethyl-3-methyl-butyl)-carbamic acid tert-butyl ester (1.9 g, 53%). ¹H NMR confirmed the compound.

[0266] Compound 56 was prepared from (1-hydroxymethyl-3-methyl-butyl)-carbamic acid tert-butyl ester following the same procedures for the preparation of 55.

[0267] Methyllithium (1M in THF) (120 mL, 3.5 eq.) was added to a solution of 4-hydroxy-cyclohexanecarboxylic acid (cis/trans mixture) (5.00 g, 1 eq.) in THF (350 mL) at −78° C. After stirring at −78° C. for 45 min, the cooling bath was removed and the resulting mixture was warmed to room temperature and stirred overnight. After total 24 h, the resulting reaction mixture was poured into ice/water (800 mL). This mixture was vigorously stirred. The separated aqueous phase was extracted with MeOH/EtOAc (˜1/20). The combined organic layer was dried over Na₂SO₄, filtered and concentrated. The crude product was purified by chromatography (50% to 100% EtOAc/hexanes) to give 1-(4-hydroxy-cyclohexyl)-ethanone (2.08 g, 42%).

[0268] A mixture of 1-(4-hydroxy-cyclohexyl)-ethanone (2.24 g, 1 eq.), toluene (160 mL), neopentylglycol (1.96 g, 1.2 eq.) and pTsOH (150 mg, 0.05 eq.) in a flask equipped with Dean-Stark apparatus was heated to reflux overnight. The mixture was cooled down to room temperature and contentrated. The crude product was purified by silic gel column chromatography (25% to 50% EtOAc/hexanes) to give 4-(2,5,5-trimethyl-[1,3]dioxan-2-yl)-cyclohexanol (2.23 g, 62%).

[0269] TPAP (161 mg, 0.05 eq.) was added to a solution of 4-(2,5,5-trimethyl-[1,3]dioxan-2-yl)-cyclohexanol (2.22 g, 1 eq.) and NMO (2.28 g, 2 eq.) in MeCN (65 mL). The reaction mixture was stirred at room temperature overnight. Saturated aqueous solution of Na₂S₂O₃ was added to the mixture and the resulting mixture was stirred vigorously for 15 minutes. The separated aqueous phase was extracted with CH₂Cl₂. The combined organic layer was dried over Na₂SO₄, filtered through Celite and concentrated. The crude product was purified by silica gel column chromatography (25% to 50% EtOAc/hexanes) to give 4-(2,5,5-trimethyl-[1,3]dioxan-2-yl)-cyclohexanone (1.87 g, 85%)

[0270] Compound 57 was prepared from 4-(2,5,5-trimethyl-[1,3]dioxan-2-yl)-cyclohexanone following the procedure for the preparation of 34 from 1,2-diphenyl-ethanone.

[0271] To a suspension of (3,3-dimethyl-1,5-dioxa-spiro[5,5]undec-9-yl)-methyl-amine hydrochloride (6.9 g, 27.6 mmol, 1.0 eq.), Et3N (15 mL, 4.0 eq.) and DMAP (catalytic amount) in THF-MDF (1:1, 100 mL) was added di-t-butyl dicarbonate (7.6 mL, 1.2 eq.) and the resulting mixture was heated at 90° C. for 6 h. After cooling to room temperature, he reaction mixture was diluted with sat. NaHCO₃ and the separated aqueous layer was extracted with 2×EtOAc. The combined organic layer was dried over Na₂SO₄, filtered and concentrated. The crude product was purified by chromatography (10% to 20% EtOAc/hexanes) to give (3,3-dimethyl-1,5-dioxa-spiro[5,5]undec-9-yl)-methyl-carbamic acid tert-butyl ester as a white solid (9.53 g, 99%).

[0272] A solution of (3,3-dimethyl-1,5-dioxa-spiro[5,5]undec-9-yl)-methyl-carbamic acid tert-butyl ester (9.53 g, 27.2 mmol, 1.0 eq.) and PPTS (2.1 g, 0.3 eq.) in acetone-water (2:1, 500 mL) was heated at 80° C. for 18 h, cooled to room temperature and concentrated to remove acetone. The residual aqueous solution was diluted with NaHCO₃ and extracted with 2×EtOAc. The combined organic layer was dried over Na₂SO₄, filtered and concentrated. The crude product was purified by chromatography (20% to 50% EtOAc/hexanes) to give methyl-(4-oxo-cyclohexyl)-carbamic acid tert-butyl ester as a white solid (5.38 g, 87%).

[0273] To a solution of methyl-(4-oxo-cyclohexyl)-carbamic acid tert-butyl ester (134 mg, 0.59 mmol, 1.0 eq.) in CH₂Cl₂ (0.5 mL) at room temperature was added (MeOCH₂CH₂)₂NSF₃ (217 μL, 2.0 eq.) followed by ethanol (10 μL, 0.3 eq.). After stirring for 1 h, the reaction was quenched carefully by addition of sat. NaHCO₃ and stirred until gas evolution ceased. The separated aqueous phase was extracted with CH₂Cl₂. The combined organic extracts were dried over Na₂SO₄, filtered and concentrated. The crude mixture was purified by chromatography (5% to 10% EtOAc/hexanes) to give mixture of (4,4-difluoro-cyclohexyl)-methyl-carbamic acid tert-butyl ester and (4-difluoro-cyclohex-3-enyl)-methyl-carbamic acid tert-butyl ester. To a solution of the mixture products in CH₂Cl₂ (1.5 mL) at room temperature was added trifluoroacetic acid (1.5 mL) at room temperature and the resulting mixture was stirred for 2.5 h and concentrated to give a mixture of 58 and 59 (2:1 ratio by H¹-NMR).

[0274] To a solution of 3-chloro-2-chloromethy-1-propene (20.0 g, 160 mmol, 1.0 eq.) in THF (40 mL) at 0° C. was added NaOMe (100 mL of 25% solution in methanol, 2.8 eq.). After cooling bath was removed, the reaction mixture was stirred at room temperature for 20 h and at 35° C. for 20 h. The reaction was quenched with sat. NH₄Cl (10 mL) and the mixture was diluted with ether (200 mL) and filtered washing with ether. The filtrate was concentrated by distillation of ether, THF and EtOH at atmospheric pressure to give light yellow liquid residue. Fractional distillation of the residue gave 3-methoxy-2-methoxymethy-1-propene (8.9 g, 43%). b.p.=120-130° C.

[0275] To a solution of the 3-methoxy-2-methoxymethy-1-propene (3.5 g, 30 mmol, 1.0 eq.) in THF (10 mL) at 0° C. was added BH₃.THF (1M in THF, 18 mL, 0.6 eq.) and the resulting mixture was stirred for 40 min. The reaction was quenched with water followed by sodium perborate (10.6 g, 2.3 eq.), warmed to room temperature, stirred overnight, diluted with CH₂Cl₂ and filtered through celite. The filtrate was diluted with brine and the separated aqueous layer was extracted with CH₂Cl₂. The combined extracts were dried over Na₂SO₄ and filtered. The filtrate was didstilled at atmospheric pressure to give light yellow liquid residue. Fractional distillation of the residue at 40 milliTorr gave 3-methoxy-2-methoxymethypropan-1-ol (1.93 g, 48%). b.p.=90-110° C.

[0276] To a solution of alcohol 3-methoxy-2-methoxymethypropan-1-ol (0.90 g, 6.7 mmol, 1.0 eq.) in CH₂Cl₂ (10 mL) at 0° C. was added Et₃N (1.9 mL, 2.0 eq.) followed by MsCl (0.63 mL, 1.2 eq.). After stirring for 40 min, the reaction was quenched with methylamine (40% in water). After concentration of the reaction mixture at room temperature, the residue was diluted with methanol (2 mL) and methylamine (3 mL, 40% in water), heated at 50° C. for 18 h cooled to room temperature, saturated with Na₂CO₃ and extracted with ether. The combined extracts were dried over Na₂SO₄ and filtered. The filtrate was didstilled at atmospheric pressure to give crude product 60 (0.78 g, 80%) as a light yellow liquid.

[0277] To a solution of trans-4-amino-cyclohexanol hydrochloride (5.0 g, 32.9 mmol, 1.0 eq.) in water (80 mL) and THF (60 mL) at room temperature was added NaHCO₃ (6.4 g, 2.3 eq.) and (Boc)₂O (14.8 mL, 2.0 eq.). After stirring for 48 h, most of THF from reaction mixture was removed by concentration and the aqueous residue was extracted with EtOAc. The combined organic extracts were dried over Na₂SO₄, filtered and concentrated. The crude product was crystallized from EtOAc-hexanes (9:1) to give (4-trans-hydroxy-cyclohexyl)-carbamic acid tert-butyl ester (5.2 g, 75%).

[0278] To a solution of (4-trans-hydroxy-cyclohexyl)-carbamic acid tert-butyl ester (3.0 g, 13.9 mmol, 1.0 eq.) and methyl iodide (4.3 mL, 5.0 eq.) in N-methyl-2-pyrrolidinone (NMP) (50 mL) at 0° C. was added 60% NaH in mineral oil (1.67 g, 3.0 eq.) in a controlled portion wise manner and the resulting mixture was stirred for 3 h at room temperature. The reaction mixture was quenched with methanol (3.0 mL), stirred for 30 min, diluted with sat. NH₄Cl and the mixture was extracted three times with EtOAc. The combined organic extracts were dried over Na₂SO₄, filtered and concentrated. The crude mixture was purified by silica gel chromatography (20% EtOAc/hexanes) to give (4-trans-methoxy-cyclohexyl)-methyl-carbamic acid tert-butyl ester (3.25 g, 96%).

[0279] To a solution of trans-(4-methoxy-cyclohexyl)-methyl-carbamic acid tert-butyl ester (445 mg, 1.83 mmol, 1.0 eq.) in CH₂Cl₂ (2 mL) at room temperature was added trifluoroacetic acid (2 mL). After stirring for 2 h, the reaction mixture was concentrated to give 61 (685 mg, 145%, contains residual TFA). ¹H NMR confirmed the structure and the product was used without further purification.

[0280] Alternatively, compound 61 may be prepared according to the following scheme:

[0281] Thus, oxidation of 4-methoxy cyclohexanol under suitable conditions (e.g., TPAP, NMO) in a suitable solvent (e.g., methylene chloride) gives the corresponding ketone. Reductive amination of 4-methoxy cyclohexanone under suitable conditions (e.g., dimethylamine, NaBH(OAc)₃, AcOH in THF) gives access to the corresponding amine 61 with good stereoselectivity (i.e., trans).

[0282] To a suspension of methyl-(4-oxo-cyclohexyl)-carbamic acid tert-butyl ester (an intermediate for the preparation of 58 and 59, 580 mg, 2.56 mmol, 1.0 eq.) in THF (8 mL) at −78° C. was added LS-selectride (1 M solution in THF, 5.7 mL, 2.2 eq.). After stirring for 2.5 h, the reaction mixture was warmed to 0° C. and stirred for 30 min. The reaction was quenched with sat. NH₄Cl and the separated aqueous layer was extracted with EtOAc-hexanes (1:1). The combined organic extracts were dried over Na₂SO₄, filtered and concentrated. The crude mixture was purified by silica gel chromatography.(33% to 50% EtOAc/hexanes) to give (4-cis-hydroxy-cyclohexyl)-methyl-carbamic acid tert-butyl ester (391 mg, 67%).

[0283] Compound 62 was prepared from (4-cis-hydroxy-cyclohexyl)-methyl-carbamic acid tert-butyl ester following the same procedure for the preparation of 61 from (4-trans-hydroxy-cyclohexyl)-carbamic acid tert-butyl ester.

[0284] To a solution of (4-cis-hydroxy-cyclohexyl)-methyl-carbamic acid tert-butyl ester (1.95 g, 8.52 mmol, 1.0 eq.) in DMF (20 mL) at 0° C. was added NaH (559 mg, 2.5 eq.). After stirring for 10 min, methyl iodide (3.9 mL, 7.6 eq.) was introduced and the cooling bath was removed. After stirring for 5 h atr room temperature, the reaction was quenched with methanol (1.5 mL), stirred for 15 min and diluted with sat. NH₄Cl. The mixture was extracted with EtOAc-hexanes (1:1). The combined organic extracts were dried over Na₂SO₄, filtered and concentrated. The crude mixture was purified by silica gel chromatography (10% to 25% EtOAc/hexanes) to give (4-cis-methoxy-cyclohexyl)-methyl-carbamic acid tert-butyl ester (1.73 g, 84%).

[0285] To a solution of (4-cis-methoxy-cyclohexyl)-methyl-carbamic acid tert-butyl ester (1.73 g, 7.12 mmol, 1.0 eq.) in CH₂Cl₂ (4 mL) at room temperature was added trifluoroacetic acid (4 mL). After stirring for 3.5 h, the reaction mixture was concentrated to give a crude product. This product was dissolved in CH₂Cl₂ (50 mL) and washed with sat. Na₂CO₃ (40 mL). The aqueos layer was back extracted with 5×CH₂Cl₂. The combined organic extracts were dried over Na₂SO₄, filtered and concentrated to give free amine 63 (1.12 g, 109%, contains residual CH₂Cl₂).

[0286] A mixture of 18 (0.01-0.1 M, 1.0 eq.), diisopropylethylamine (5.0 eq.) and any one of amine from 21-63 or other commercially available primary or secondary alkylamine (3-10 eq.) in dichloromethane was stirred at room temperature or at 40° C. for several hours to five days until reaction was completed. The reaction mixture was concentrated and the intermediate product, either with or without purification by chromatography (EtOAc/hexanes), was dissolved in 1:1 mixture of dichloromethane and trifluoroacetic acid (0.05 M) and stirred at room temperature with or without anisole (5-10 eq.) for 3-4 h until reaction was completed. The reaction was then carefully quenched with sat. NaHCO₃, extracted with EtOAc until there was no product detected. The combined extracts were dried over Na₂SO₄, filtered, concentrated and the product 64 was purified by reverse phase HPLC (MeOH-water).

[0287] The following procedure has been used for aromatic amines (R_(F) and/or R_(G)=Ar). To a solution of N-ethylaniline (47 μL, 6 eq.) in THF (1 mL) at −78° C. was added nBuLi (148 μL, 2.5 M in hexanes, 6 eq.) followed by HMPA (200 μL) and stirred for 10 min. A solution of 18 (44 mg, 0.062 mmol) in THF (0.7 mL) was introduced by rinsing with THF (0.3 mL). After 10 min stirring, the reaction mixture was quenched with sat. NaHCO₃ (15 mL), extracted with 3×EtOAc. The combine extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatography (EtOAc) to give an intermediate. This intermediate and anisole (100 μL) was dissolved in 1:1 mixture of dichloromethane and trifluoroacetic acid (2 mL) and stirred at room temperature 3 h. The reaction was then carefully quenched with sat. NaHCO₃, extracted with 4×EtOAc. The combine extracts were dried over Na₂SO₄, filtered, concentrated and the product 64 was purified by reverse phase HPLC (MeOH-water).

[0288] Diisopropylethylamine (1.6 eq.) was added to a solution of 20 (0.03-0.05 M, 1.0 eq.) and TOTU (1.5 eq.) in DMF at room temperature and stirred for 15 min. To the resulting mixture was added any one amine from 21-63 or other commercially available primary or secondary amine (1.5 eq.). The reaction mixture was stirred for several hours to overnight until reaction completed. The reaction mixture was concentrated and the intermediate product, either with or without purification by chromatography (EtOAc/hexanes), was dissolved in 1:1 mixture of dichloromethane and trifluoroacetic acid (0.01-0.05M) and stirred at room temperature with or without anisole (5-10 eq.) for 3-4 h until reaction was completed. The reaction was then carefully quenched with sat. NaHCO₃, extracted with EtOAc until there was no product detected. The combine extracts were dried over Na₂SO₄, filtered, concentrated and the product 65 was purified by reverse phase HPLC (MeOH-water).

[0289] Compounds in the following table were prepared either following the preparation of 13 or 64 or 65. Compound # MS (ES) (ER # or Or/And IC#) Structure of 64 or 65 ¹HNMR 806094

¹H NMR 806095

¹H NMR 806123

361.4 (M + H)⁺ 806136

404.3 (M + H)⁺ 806181

¹H NMR 806221

413.3 (M + H)⁺ 806220

465.3 (M + H)⁺ 806224

409.3 (M + H)⁺ 806228

412.3 (M + H)⁺ 806276

471.3 (M + H)⁺ 806275

487.3 (M + H)⁺ 806274

397.3 (M + H)⁺ 806273

411.3 (M + H)⁺ 806317

398.2 (M + H)⁺ 806320

417.2 (M + H)⁺ 806329

424.3 (M + H)⁺ 806333

497.3 (M + H)⁺520.2 (M + Na)⁺ 806336

411.3 (M + H)⁺ 806358

397.2 (M + H)⁺ 806359

383.3 (M + H)⁺ 806363

462.2 (M + H)⁺ 806362

440.3 (M + H)⁺ 806361

479.2 (M + H)⁺ 806368

369.2 (M + H)⁺ 806372

495.2 (M + H)⁺ 806373

499.2 (M + H)⁺ 806374

483.2 (M + H)⁺ 806375

384.3 (M + H)⁺ 806383

363.3 (M + H)⁺ 806393

512.2 (M + H)⁺ 806402

411.2 (M + H)⁺433.2 (M + Na)⁺ 806417

397.1 (M + H)⁺ 806419

469.2 (M + H)⁺ 806421

511.2 (M + H)⁺ 806435

411.3 (M + H)⁺ 806437

411.3 (M + H)⁺ 806569

452.3 (M + H)⁺ 806609

495.3 (M − H)⁻ 806610

425.4 (M − H)⁻ 806647

496.3 (M + H)⁺ 806653

454.3 (M + H)⁺ 806671

409.3 (M + H)⁺ 806781

¹H NMR 806790

509.3 (M − H)⁻ 806796

¹H NMR 806820

496.3 (M + H)⁺ 806839

467.2 (M + Na)⁺ 806840

467.2 (M + Na)⁺ 806841

445.3 (M + H)⁺ 806842

397.3 (M + H)⁺ 806843

483.3 (M + H)⁺505.3 (M + Na)⁺ 806844

363.3 (M + H)⁺385.3 (M + Na)⁺ 806860

496.3 (M + H)⁺ 806874

¹H NMR 806875

¹NMR 806878

¹H NMR 806899

¹H NMR 806900

¹H NMR 806901

497.1 (M + H)⁺ 806902

377.3 (M + H)⁺ 806903

431.1 (M + H)⁺ 806904

431.2 (M + H)⁺ 806905

431.2 (M + H)⁺ 806987

441.3 (M + H)⁺ 807014

343.3 (M + Na)⁺ 807139

¹H NMR 807140

427.3 (M + H)⁺ 807183

463.3 (M + Na)⁺441.3 (M + H)⁺ 807240

427.2 (M + H)⁺ 807377

¹H NMR 807392

¹H NMR 807400

¹H NMR 807401

¹H NMR 807399

¹H NMR 807447

¹H NMR 807448

¹H NMR 807449

¹H NMR 807450

481.1 (M + H)⁺ 807451

481.1 (M + H)⁺ 807452

465.1 (M + H)⁺ 807453

¹H NMR 807454

¹H NMR 807457

¹H NMR 807458

¹H NMR 807459

¹H NMR 807460

481.1 (M + H)⁺ 807460

¹H NMR 807463

¹H NMR 807464

¹H NMR 807465

¹H NMR 807466

¹H NMR 807467

¹H NMR 807469

¹H NMR 807497

¹H NMR 807498

¹H NMR 807505

¹H NMR 807506

¹H NMR 807528

¹H NMR 807531

¹H NMR 807532

¹H NMR 807543

¹H NMR 807544

¹H NMR 807548

¹H NMR 807549

¹H NMR 807550

¹H NMR 807562

¹H NMR 807571

¹H NMR 807573

387.3 (M + H)⁺ 807586

¹H NMR 807636

¹H NMR 807649

¹H NMR 807660

¹H NMR 807662

¹H NMR 807663

¹H NMR 807703

¹H NMR 807704

¹H NMR 807748

¹H NMR 807749

¹H NMR 807751

¹H NMR 807754

¹H NMR 807758

¹H NMR 807762

¹H NMR 807779

¹H NMR 807794

¹H NMR 807836

¹H NMR 807862

¹H NMR 807876

¹H NMR 807892

¹H NMR 807920

¹H NMR 807930

¹H NMR 807931

¹H NMR 807952

¹H NMR 807956

¹H NMR 807962

¹H NMR 807977

¹H NMR 807978

¹H NMR 807980

¹H NMR 808028

¹H NMR 808039

¹H NMR 808069

¹H NMR 808078

¹H NMR 808079

¹H NMR 808084

¹H NMR 808086

¹H NMR 808101

¹H NMR 808102

¹H NMR 808107

¹H NMR 808151

¹H NMR 808153

¹H NMR 808164

¹H NMR 808247

¹H NMR 808254

¹H NMR 808255

¹H NMR 808283

¹H NMR 808290

¹H NMR 808312

¹H NMR 808313

¹H NMR 808346

¹H NMR 808347

¹H NMR 808355

¹H NMR 808356

¹H NMR 808364

¹H NMR 808365

¹H NMR 808371

¹H NMR 808387

¹H NMR 808548

¹H NMR 808661

¹H NMR 808663

¹H NMR 808665

¹H NMR 808675

¹H NMR 808702

¹H NMR 808833

¹H NMR 808836

¹H NMR 808984

¹H NMR

[0290]

[0291] Diethyl azodicarboxylate (9.1 μL, 2.0 eq.) was added to a solution of 17 (20 mg, 0.03 mmol, 1.0 eq.), triphenylphosphine (15 mg, 2.0 eq.) and phthalimide (8.5 mg, 2.0 eq.) in toluene (2 mL) at room temperature and the resulting mixture was stirred for 19 h. The reaction mixture was concentrated and the intermediate was purified by chromatography (30% EtOAc-hexanes) to give 19.3 mg (81%). This intermediate was dissolved in 1:1 mixture of dichloromethane and trifluoroacetic acid (2 mL) and stirred at room temperature for 2 h until reaction was completed. The reaction was then carefully quenched with sat. NaHCO₃ (15 mL), extracted with 7×10 mL of EtOAc. The combine extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by reverse phase HPLC (MeOH-water) to give ER-806286 (2.4 mg, 24%). MS (ES) 423.2 (M+H)⁺.

[0292] Compound ER-806287 was prepared from 4-trifluoromethylphenol following the same procedure for the preparation of ER-806286. MS (ES) 438.2 (M+H)⁺.

[0293] A mixture of 18 (12.5 mg, 0.018 mmol), diisopropylethylamine (0.2 mL, 65 eq.) and thiophenol (10 μL, 5.5 eq.) in DMF (0.5 mL) at room temperature was stirred for two days. The reaction mixture was concentrated and purified by chromatography (30% EtOAc-hexanes) to give an intermediate 12.7 mg (92%). This intermediate and anisole (100 μL) were dissolved in 1:1 mixture of dichloromethane and trifluoroacetic acid (2 mL) and stirred at room temperature for 40 min. The reaction was then carefully quenched with sat. NaHCO₃ (15 mL), extracted with 7×EtOAc. The combine extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatography (5% MeOH-EtOAc) to give ER-806311 (4.5 mg, 65%). MS (ES) 386.2 (M+H)⁺.

[0294] Methylsulfonyl chloride (9 μL, 2 eq.) was added to a solution of 17 (40.5 mg, 0.058 mmol) and diisopropylethylamine (100 μL, 10 eq.) in dichloromethane (1 mL) at 0° C. and stirred for 30 min. 4-hydroxypiperidine (30 mg, 5.0 eq.) and DMF (0.5 mL) were introduced and the reaction mixture was warmed to room temperature and stirred for 2.5 days. The reaction was quenched with sat. NaHCO₃ (10 mL) and the separated aqueous phase was extracted with 4×EtOAc. The combine organic extracts were dried over Na₂SO₄, filtered and concentrated and the product was purified by reverse HPLC (MeOH-water) to give an intermediate (25 mg, 65%). This intermediate was dissolved in dichloromethane (0.5 mL) and treated with TPAP (5 mg) and NMO (20 mg) at room temperature for 10 min. The reaction was quenched by addition of water and Na₂S₂O₃ extracted with 4×EtOAc. The combine organic extracts were dried over Na₂SO₄, filtered and concentrated and the product was purified by chromatography (15% EtOAc-hexanes) to give an intermediate (13.7 mg). This intermediate and anisole (100 μL) were dissolved in dichloromethane (1 mL) and treated with trifluoroacetic acid (1 mL) at room temperature for 4 h. The reaction was then carefully quenched with sat. NaHCO₃ (15 mL), extracted with 4×EtOAc. The combine extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by reverse phase HPLC (MeOH-water) to give ER-806355 (3.4 mg, 16% for three steps). ¹H NMR (DMSO-d₆) δ 2.35 (t, J=6 Hz, 4H), 2.49 (s, 3H), 2.70 (t, J=6 Hz, 4H), 3.67 (s, 2H), 5.74 (s, 2H), 6.73 (s, 1H), 7.16 (dd, J=8.2 and 1.2 Hz, 1H), 7.28 (d, J=1.2 Hz, 1H), 7.53 (d, J=8.2, 1H), 7.55 (s, 1H).

[0295] Hydrogen peroxide (4 mL, 30% in water, 3.6 eq.) was added to a solution of thiomorpholine (1.0 g, 9.7 mmol) in acetic acid (12 mL) at room temperature. The resulting mixture was stirred at 100° C. overnight, cooled to room temperature and concentrated. Thiomorpholine sulfoxide from the residue was crystallized from ethanol as a deep colored solid. Following the general procedure for the preparation of 64, compound ER-806401 was prepared from 18 and Thiomorpholine sulfoxide. MS (ES) 417.2 (M+Na)⁺.

[0296] A mixture of 18 (5 mg) and benzyl alcohol (100 μL) was treated with tBuOK (1 mL, 1.66 M in THF) at room temperature overnight. The reaction mixture was quenched with sat. NaHCO₃ and extracted with 3×EtOAc. The combine extracts were dried over Na₂SO₄, filtered, concentrated and the crude intermediate and anisole (50 μL) were dissolved in dichloromethane (0.5 mL) and treated with trifluoroacetic acid (0.5 mL) at room temperature for 3 h. The reaction was then carefully quenched with sat. NaHCO₃, extracted with 4×EtOAc. The combine extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by thin layer chromatograph (10% MeOH/EtOAc) to give ER-806404 (1.0 mg, 37%). MS (ES) 384.2 (M+H)⁺.

[0297] To a solution of 5-iodoindole (5.0 g, 20.6 mmol), phenylacetylene (3.4 mL, 1.5 eq.) and diethylamine (10 mL) in DMF (2 mL) was added Pd(Ph₃P)₄ (120 mg, 0.005 eq.) and CuI (39 mg, 0.01 eq.) under nitrogen atmosphere at cooling water both temperature and the resulting mixture was stirred for 3 h at room temperature. The reaction was diluted with sat. NaHCO₃ (50 mL), extracted with 4×30 mL of EtOAc. The combined extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatograph (15 to 20% EtOAc/hexanes) to give 5-phenylethynyl-1H-lindole (4.41 g, 98%).

[0298] Compound 5-phenylethynyl-lindole-1-carboxylic acid tert-butyl ester was prepared from 5-phenylethynyl-1H-lindole following the procedure for the preparation of 7 (indole-1,5-dicarboxylic acid 1-tert-butyl ester 5-methyl ester as an example) from methyl indole-5-carboxylate.

[0299] Compound 5-phenylethynyl-2-tributylstannanyl-indole-1-carboxylic acid tert-butyl ester was prepared from 5-phenylethynyl-lindole-1-carboxylic acid tert-butyl ester following the procedure for the preparation of 10 from 9.

[0300] Compound ER-806644 was prepared from 5-phenylethynyl-2-tributylstannanyl-indole-1-carboxylic acid tert-butyl ester and 4 (R₁=Me) following the procedure for the preparation of 13. MS (ES) 364.2 (M+H)⁺.

[0301] A solution of ER-806644 (6.5 mg) and Lindlar catalyst (50 mg) in THF (2 mL) was stirred at room temperature under hydrogen gas for 1 h. The resulting mixture was filtered through celite and the filtrate was concentrated. The residual solid was washed several times with EtOAc to give ER-806645 as a light yellow solid (2.0 mg, 31%). MS (ES) 366.3 (M+H)⁺.

[0302] A solution of ER-806644 (5 mg) and Pd(OH)₂ (10 mg) in THF (2 mL) was stirred at room temperature under hydrogen gas for overnight. The resulting mixture was filtered through celite and the filtrate was concentrated and the product was purified by reverse phase HPLC (MeOH-water) to give ER-806646 (1.3 mg, 26%). MS (ES) 368.3 (M+H)⁺.

[0303] A solution of 16 (20 mg) in 1:1 THF-MeOH (3 mL) at room temperature was treated with a solution of 1 N HCl (0.5 mL) for 30 min. The reaction mixture was diluted with sat. NaHCO₃ and extracted with EtOAc. The combined extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by reverse phase HPLC (MeOH-water) to give ER-806095 (2.6 mg, 18%). ¹H NMR.

[0304] A solution of ER-806393 (1.3 mg) in MeOH (0.5 mL) was treated at room temperature with a solution of 1 N LiOH (0.1 mL) for overnight. The reaction mixture was then neutralized with a solution of 1 N HCl (0.1 mL) to pH=5 and concentrated. The residue was taken up in 1:1 MeOH-EtOAc and filtered. The filtrate was concentrated and purified by reverse phase HPLC (MeOH-water) to give ER-806420 (0.5 mg, 40%). MS (ES) 496.3 (M−H)⁻.

[0305] A mixture of 18 (15.5 mg, 0.02 mmol) and methylamine (0.11 mL, 2.0 M in THF, 1.0 eq.) in dichloromethane (0.5 mL) was stirred at room temperature overnight, diluted with sat.NaHCO₃ and extracted with 3×EtOAc. The combined extracts were dried over Na₂SO₄, filtered and concentrated. The residue was dissolved in DMF (0.5 mL) as a solution A.

[0306] Diisopropylethylamine (5.3 μL, 1.4 eq.) was added to a solution of benzoic acid (3.4 mg, 1.3 eq.) and TOTU (10 mg, 1.4 eq.) in DMF (0.3 mL) at room temperature and stirred for 15 min. Solution A was then introduced by rinsing with 3×0.5 mL of DMF and the resulting mixture was stirred overnight, concentrated, diluted with sat.NaHCO₃ and extracted with 3×EtOAc. The combined extracts were dried over Na₂SO₄, filtered and concentrated. The residue and anisole (50 μL) was dissolved in dichloromethane (0.5 mL) and treated with trifluoroacetic acid (0.5 mL) at room temperature for 3 h. The reaction mixture was carefully quenched with sat.NaHCO₃ and EtOAc and the separated aqueous phase was extracted with 3×EtAOc. The combined extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by reverse phase HPLC (MeOH-water) to give ER-806432 (1.4 mg, 16% for three steps). MS (ES) 411.2 (M+H)⁺.

[0307] 5-nitro-indole-1-carboxylic acid tert-butyl ester was prepared from 5-nitroindole following the same procedure for the preparation of 7 from methyl indole-5-carboxylate.

[0308] A solution of 5-nitro-indole-1-carboxylic acid tert-butyl ester (0.50 g) and catalytic amount of Pd(OH)₂ in a mixture of MeOH-EtOAc was stirred at room temperature under hydrogen for 1 h. The reaction mixture was filtered through celite and the filtrate was concentrated to provide 5-amino-2,3-dihydro-indole-1-carboxylic acid tert-butyl ester (0.44 g, 98%).

[0309] Benzoyl chloride (305 μL, 1.5 eq.) was added to a solution of 5-amino-2,3-dihydro-indole-1-carboxylic acid tert-butyl ester (407 mg, 1.74 mmol) and triethylamine (1.2 mL, 5.0 eq.) in dichloromethane (5 mL) at 0° C. and the resulting mixture was stirred for 15 min. The reaction was then quenched by addition of sat. NaHCO₃ and the mixture was extracted with 3×EtOAc. The combined extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatography (20 to 100% EtOAc-hexanes) to give 5-benzoylamino-2,3-dihydro-indole-1-carboxylic acid tert-butyl ester (588 mg, 100%).

[0310] Sodium hydride (60 mg, 1.5 eq.) was added to a mixture of 5-benzoylamino-2,3-dihydro-indole-1-carboxylic acid tert-butyl ester (570 mg, 1.68 mmol) and methyl iodide (0.42 mL, 4.0 eq.) in DMF (10 mL) at 0° C. and the resulting mixture was stirred for 20 min. After concentration, the residue from reaction mixture was diluted with sat. NaHCO₃ and extracted with 3×EtOAc. The combined extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by chromatography (30% EtOAc-hexanes) to give 5-(benzoyl-methyl-amino)-2,3-dihydro-indole-1-carboxylic acid tert-butyl ester (547 mg, 93%).

[0311] A mixture of 5-(benzoyl-methyl-amino)-2,3-dihydro-indole-1-carboxylic acid tert-butyl ester (500 mg) and MnO₂ (5 g) in toluene (20 mL) was heated at 80° C. for 1 h. Additional MnO₂ (5 g) was introduced and the resulting mixture was stirred at 80° C. for 1 h. After cooling to room temperature, the mixture was filtered through celite and the filtrate was concentrated. The product was purified by chromatography (30% EtOAc-hexanes) to give 5-(benzoyl-methyl-amino)-indole-1-carboxylic acid tert-butyl ester (372 mg, 75%).

[0312] 5-(benzoyl-methyl-amino)-2-tributylstrannanyl-indole-1-carboxylic acid tert-butyl ester was prepared from 5-(benzoyl-methyl-amino)-indole-1-carboxylic acid tert-butyl ester following the procedure for the preparation of 10 from 9.

[0313] Compound ER-807313 was prepared from 5-(benzoyl-methyl-amino)-2-tributylstrannanyl-indole-1-carboxylic acid tert-butyl ester and 4 (R₁=Me) following the procedure for the preparation of 13. MS (ES) 397.2 (M+H)⁺ and 419.1 (M+Na)⁺.

[0314] Compound ER-807015 was prepared as a by-product during preparation of 65 from sterically hindered amines and yielded a satisfactory ¹H NMR spectrum.

[0315] A mixture of 18 (51 mg, 1.0 eq.), (3,3-dimethyl-1,5-dioxa-spiro[5,5]undec-9-yl)-methyl-amine hydrochloride (71 mg, 4.0 eq.), ethyldiisopropylamine (0.25 mL, 20 eq.) and DMF (0.3 mL) in CH₂Cl₂ (2.5 mL) was stirred at room temperature for 23 h. After concentration, the residue was dissolved in 1 N HCl (0.6 mL) and acetone (0.6 mL) and heated at reflux for 16 h. After cooling to room temperature, the reaction was then carefully quenched with sat. NaHCO₃, extracted with EtOAc until there was no product detected. The combine extracts were dried over Na₂SO₄, filtered, concentrated and the product was purified by reverse phase HPLC (MeOH-water) to give ER-807586 (6.4 mg, 22%). ¹HNMR and MS (ES) 403.5 (M +H)⁺.

[0316] ER-807759 was prepared following the same procedure for 13 (ER-805639 as an example) in Stille coupling reaction and for ER-807586 in ketal hydrolysis reaction. ¹HNMR and MS (ES) 389 (M+H)⁺.

[0317] To a suspension of ER-807586 (5 mg, 0.0124 mmol, 1.0 eq.) in water (0.5 mL) was added NH₂OMeHCl (5.2 mg, 0.623 mmol, 50 eq.). The solid became soluble and saturated NaHCO₃ (0.3 mL) was slowly added and the resulting mixture was stirred overnight. The reaction mixture was diluted with EtOAc and saturated NaHCO₃, and extracted with 4×EtOAc. The organic layers were combined, dried over MgSO₄, filtered and concentrated. The crude mixture was purified by silica gel chromatography (10% MeOH-EtOAc) to give ER-807789 as a white solid (5.3 mg, 100%). 1HNMR and MS (ES) 432 (M+H)⁺.

[0318] To a solution of ER-807586 (15 mg) in MeOH-THF (1:1, 1 mL) was added NaBH₄ (20 mg) and the mixture was stirred for 30 min, diluted with saturated NaHCO₃ and extracted with 4×EtOAc. The organic layers were combined, dried over MgSO₄, filtered and concentrated. The crude mixture was purified by reverse HPLC (MeOH-H₂O) to give ER-807790. ¹HNMR and MS (ES) 405.5 (M+H)⁺.

[0319] To a solution of n-BuLi (1.6 M in hexanes, 0.35 mL, 0.56 mmol, 31.3 eq.) in THF (2.0 mL) at 0° C. was added methyl triphenylphosphonium bromide (0.20 g, 0.56 mmol, 31 eq.). The reaction was wormed to room temperature and stirred for 40 minutes. A portion of the solution (0.6 mL) was transferred to another flask and ER-807586 (7.2 mg, 0.0179 mmol, 1.0 eq.) was added. The resulting mixture was stirred at room temperature for 18 hours and water was added and the mixture was extracted with 3×EtOAc. The organic layers were combined, dried over MgSO₄, filtered and concentrated. The crude mixture was purified by reverse HPLC (MeOH-H₂O) to give ER-807835 (0.8 mg, 12%). ¹H NMR and MS (ES) 401.5 (M+¹H).

[0320] To a solution of ER-807586 (11.5 mg, 0.0286 mmol, 1.0 eq.) in THF (2.0 mL) at 0° C. was added MeMgCl (3.0 M in THF, 0.25 mL, 0.75 mmol, 26.3 eq.). The reaction was warmed and stirred at room temperature for 18 hours. The reaction was quenched with saturated NaHCO₃, and then was extracted with 3×EtOAc. The organic layers were combined, dried over MgSO₄, filtered and concentrated. The resulting mixture was purified by silica gel chromatography (100% EtOAc, then 10% to 30% MeOH-EtOAc) to give ER-807837 (0.8 mg, 7%). ¹H NMR and MS (ES) 419.4 (M+¹H).

[0321] 5-chloromethyl-indole-1-carboxylic acid tert-butyl ester was prepared from 8 following the procedure for the preparation of 9 but without the addition of morpholine.

[0322] A mixture of 5-chloromethyl-indole-1-carboxylic acid tert-butyl ester (0.82 g, 3.10 mmol, 1.0 eq.), cyclohexyl mercaptan (0.53 mL, 1.4 eq.) and K₂CO₃ (0.90 g, 2.0 eq.) in DMF (6 mL) was heated at 40° C. until reaction completed. The reaction mixture was cooled to room temperature, diluted with sat. NH₄Cl and extracted with diethyl ether. The organic extracts were dried over MgSO₄, filtered and concentrated. The resulting mixture was purified by chromatography (5% EtOAc/hexanes) to give 5-cyclohexylsulfanylmethyl-indole-1-carboxylic acid tert-butyl ester (0.79 g, 74%).

[0323] ER-808036 was prepared from 5-cyclohexylsulfanylmethyl-indole-1-carboxylic acid tert-butyl ester following the procedures for the preparation of 16 from 14.

[0324] To a solution of ER-808036 (60 mg, 0.15 mmol, 1.0 eq.) in THF (2.5 mL) and MeOH (1.5 mL) at −78° C. was added a solution of mCPBA (60 mg, ˜70%, 1.6 eq.) in THF. After stirring for 2 h, the reaction was quenched by addition of sat. Na₂S₂O₃ and sat NaHCO₃. The separated aqueous layer was extracted with 5×EtOAc, and the combined organic phase was dried over Na₂SO₄, filtered and concentrated. The crude mixture was purified by chromatography (5% to 10% MeOH/EtOAc) to give semipure products (18 mg and 32 mg each). After further purification by reverse phase HPLC (MeOH-water), ER-808082 (3.2 mg) and ER-808083 (3.2 mg) were obtained. ¹NMR confirmed both of the products.

[0325] A mixture of 5-chloromethyl-indole-1-carboxylic acid tert-butyl ester (0.41 g, 1.55 mmol, 1.0 eq.), cyclohexanol (0.82 mL, 5.0 eq.) and Ag₂O (1.80 g, 5.0 eq.) in diethyl ether (5 mL) was stirred at 35° C. over weekend. After cooling to room temperature, the reaction mixture was filtered through celite washing with ether. The filtrate was concentrated and the residue was purified by chromatography (3% EtOAc/hexanes) to give N-Boc-5-cyclohexyloxymethylindole (160 mg, 28%) as colorless oil. ¹HNMR comfirmed the compound.

[0326] ER-808103 was prepared from 5-cyclohexyloxylmethyl-indole-1-carboxylic acid tert-butyl ester following the procedures for the preparation of 16 from 14. Both MS (ES) and ¹HNMR comfirmed the compound.

[0327] To a suspension of compound 3 (R=Me, 300 mg, 1.03 μmol, 1.0 eq.) in THF (5 mL) at room temperature was added dropwise LiAH₄ (1.0 M in THF, 2.56 mL, 2.5 eq.) and the resulting mixture was then heated at 65° C. for 30 min. Afetr cooling to 0° C., the reaction was quenched by addition of MeOH (1.2 mL, 30 eq.) and water (30 eq.), stirred and warmed to room temperature and filtered through celite washing with EtOAc. The filtrate was concentrated and the residue was purified by silica gel chromatography (EtOAc then 10% MeOH-EtOAc) to give 7-chloro-2-methyl-5-methylamino-3H-imidazo[4,5-b]pyridine as a white solid (190 mg, 94%).

[0328] ER-808040 was prepared from 7-chloro-2-methyl-5-methylamino-3H-imidazo[4,5-b]pyridine and 5-[(cyclohexyl-methyl-amino)-methyl]-2-tributylstannanyl-indole-1-carboxylic acid tert-butyl ester (prepared from 8 and cyclohexyl-methyl-amine following the procedures for the preparation of 10) following the procedure for the preparation of 13. ¹HNMR confirmed the compound.

[0329] To a solution of ER-807790 (17 mg, 0.042 mmol, 1.0 eq.) in CH₂Cl₂ (1 mL) at 0° C. was added (MeOCH₂CH₂)₂NSF₃ (14 μL, 1.8 eq.) and the resulting mixture was stirred for 1 h at 0° C. and 1 h at room temperature. The reaction was quenched with sat. NaHCO₃ and the separated aqueous layer was extractred with CH₂Cl₂ followed by EtOAc-THF (1:1). The combined organic extracts were dried over Na₂SO₄, filtered and concentrated. The residue was purified by reverse HPLC (MeOH-water) to give ER-808128 (2 mg, 13%). ¹H NMR and MS confirmed the structure.

[0330] 5-formyl-indole-1-carboxylic acid tert-butyl ester or 6-formyl-indole-1-carboxylic acid tert-butyl ester

[0331] To a solution of the 8 (8.0 g, 32.4 mmol, 1 eq.) in CH₂Cl₂ (24 mL) was added portionwise Dess-Martin reagent (17.9 g, 1.3 eq.) at 0° C. and the resulting mixture was warmed slowly to room temperature and stirred for 30 min. The reaction mixture was diluted with Et₂O (100 mL), filtered through celite rinsing with Et₂O (50 m). The filtrate was washed with sat. NaHCO₃, dried over Na₂SO₄, filtered and concentrated. The crude product was azeotroped with tolune to give 5-formyl-indole-1-carboxylic acid tert-butyl ester (7.3 g, 95%) or similarly 6-formyl-indole-1-carboxylic acid tert-butyl ester

[0332] Mg (turnings) was activated by washing with 1N HCl and Et₂O, and dried on high vacuum overnight. Bromomethylcyclohexane (0.8 mL, 1 eq.) in Et₂O (4 mL) was added to the activated Mg (418 mg, 3 eq.) in Et₂O (10 mL) slowly to keep the internal temperature at 30-33° C. The resulting reaction mixture was heated at 34° C. for 1 h and cooled to 0° C. A solution of 5-formyl-indole-1-carboxylic acid tert-butyl ester (900 mg) in Et₂O (15 mL) was then introduced and the resulting mixture was warmed to room temperature, heated at 30-32° C. for 4 h, cooled to room temperature and then quenched with the addition of sat. NH₄Cl. The separated aqueous phase was extracted with EtOAc, the combined organic layer was dried over MgSO₄, filtered and concentrated. The crude product was purified by chromatography (10% to 25% EtOAc/hexanes) to give the corresponding alcohol (949 mg, 85%).

[0333] To a mixture of the alcohol (513 mg, 1 eq.) and Et₃N (625 μL, 3 eq.) in CH₂Cl₂ (15 mL) at 0° C. was added methanesulfonic anhydride (390 mg, 1.5 eq.). The cooling bath was removed and the resulting mixture was stirred for 2.5 h and diluted with sat. NaHCO₃. The separated aqueous layer was extracted with CH₂Cl₂. The combined organic layer was dried over Na₂SO₄, filtered and concentrated. The crude product was purified by chromatography (hexanes to 10% EtOAc/hexanes) to give 5-(2-cyclohexyl-vinyl)-indole-1-carboxylic acid tert-butyl ester (380 mg, 78%).

[0334] ER-808281 was prepared from 5-(2-cyclohexyl-vinyl)-indole-1-carboxylic acid tert-butyl ester following the procedures for the preparation of 16 from 14. MS (ES) and ¹HNMR confirmed the compound.

[0335] A solution of ER-808281 (˜10 mg, 1 eq.) in MeOH (5 mL) with 10% Pd/C (catalytic) was kept under positive H₂ atmosphere overnight at room temperature. The mixture was then loaded onto silica gel eluting with EtOAc to 20% MeOH/EtOAc to give ER-808469 (7.5 mg). MS (ES) and ¹HNMR confirmed the compound.

[0336] 5-vinyl-indole-1-carboxylic acid tert-butyl ester or 6-vinyl-indole-1-carboxylic acid tert-butyl ester

[0337] T a suspension of methyltriphenylphosphonium bromide (8.1 g, 22.7 mmol) in THF (140 mL) at 0° C. was added nBuLi (1.6 M in hexanes, 14.2 mL, 22.7 mmol) dropwise over 10 min. After 20 min of stirring, a solution of the 5-formyl-indole-1-carboxylic acid tert-butyl ester (4.63 g, 14.8 mmol) in THF (20 mL) was introduced slowly over 20 min. The reaction was warmed slowly to room temperature, stirred 30 min. The reaction mixture was poured into saturated ammonium chloride and the separated aqueous phase was extracted with ethylacetate (3×100 mL). The combined organic phase was dried over sodium sulfate, filtered and concentrated. The residue was purified by chromatography (methylene chloride to 1% acetone-methylene chloride) to give 5-vinyl-indole-1-carboxylic acid tert-butyl ester (4.7 g, 100%) or similarly 6-vinyl-indole-1-carboxylic acid tert-butyl ester.

[0338] 5-(2-hydroxy-ethyl)-indole-1-carboxylic acid tert-butyl ester or 6-(2-hydroxy-ethyl)-indole-1-carboxylic acid tert-butyl ester

[0339] To a solution of 5-vinyl-indole-1-carboxylic acid tert-butyl ester (4.5 g, 18.5 mmol, 1.0 eq.) in THF (46 mL) at 0° C. was added 9-BBN (0.5 M in THF, 87 mL, 2.4 eq.) over 10 min. The resulting reaction mixture was stirred for 2.5 h and diluted with THF (150 mL) and water (150 mL) while keeping the temperature at 0° C. Then NaBO₃.4H₂O (44 g) was introduced and resulting reaction mixture was stirred and warmed to room temperature and stirred. The reaction mixture was diluted with methylene chloride (100 mL) and the separated aqueous layer was extracted 3×100 mL methylene chloride. The combined organic layers were dried over sodium sulfate, filtered and concentrated. The residue was purified by chromatography (methylene chloride to 5% acetone/methylene chloride) to give 5-(2-hydroxy-ethyl)-indole-1-carboxylic acid tert-butyl ester (3.82 g, 76%) or similarly 6-(2-hydroxy-ethyl)-indole-1-carboxylic acid tert-butyl ester.

[0340] 5-(2-morpholin-4-yl-ethyl)-indole-1-carboxylic acid tert-butyl ester or 5-[2-(cyclohexyl-methyl-amino)-ethyl]-indole-1-carboxylic acid tert-butyl ester or 6-(2-morpholin-4-yl-ethyl)-indole-1-carboxylic acid tert-butyl ester or 6-[2-(cyclohexyl-methyl-amino)-ethyl]-indole-1-carboxylic acid tert-butyl ester

[0341] To a solution of 5-(2-hydroxy-ethyl)-indole-1-carboxylic acid tert-butyl ester (260 mg, 1 mmol, 1.0 eq.), triphenyl phosphine (391 mg, 1.5 eq.) and Imidazole (136 mg, 2 eq.) in methylene chloride (5 mL) was added iodine (328 mg, 1.3 eq.) in small portions over 20 min at room temperature. The reaction mixture was poured into water and extracted with 4×100 mL of methylene chloride. The combined organic phase was dried over sodium sulfate, filtered and concentrated. The residue was purified by silica gel chromatography (20% EtOAc/hexanes) to give a semipure iodide (600 mg). This iodide was then dissolved in MeOH (10 mL) and treated with morphoiline (1.73 mL, 20 eq.) at 60° C. for overnight. The reaction mixture was cooled to room temperature, poured into water and extracted with methylene chloride. The combined organic layers were dried over sodium sulfate, filtered and concentrated. The residue was purified by silica gel column chromatography (methylene chloride to 15% acetone/methylene chloride) to give 5-(2-morpholin-4-yl-ethyl)-indole-1-carboxylic acid tert-butyl ester (290 mg, 88%) or similarly or 5-[2-(cyclohexyl-methyl-amino)-ethyl]-indole-1-carboxylic acid tert-butyl ester or 6-(2-morpholin-4-yl-ethyl)-indole-1-carboxylic acid tert-butyl ester or 6-[2-(cyclohexyl-methyl-amino)-ethyl]-indole-1-carboxylic acid tert-butyl ester.

[0342] 5-(2-methoxycarbonyl-vinyl)-indole-1-carboxylic acid tert-butyl ester or 6-(2-methoxycarbonyl-vinyl)-indole-1-carboxylic acid tert-butyl ester

[0343] To a solution of the 5-formyl-indole-1-carboxylic acid tert-butyl ester (3.4 g, 13.8 mmol, 1.0 eq.) in toluene (35 mL) was added Ph₃P=CHCO₂Me (5.5 g, 1.2 eq.) at room temperature and the resulting mixture was stirred overnight. After concentration, the crude product purified by silica gel column chromatography (methylene chloride to 1% acetone-methylene chloride) to give 5-(2-methoxycarbonyl-vinyl)-indole-1-carboxylic acid tert-butyl ester (5.03 g, 90%) or similarly 6-(2-methoxycarbonyl-vinyl)-indole-1-carboxylic acid tert-butyl ester.

[0344] 5-(3-hydroxy-propenyl)-indole-1-carboxylic acid tert-butyl ester or 6-(3-hydroxy-propenyl)-indole-1-carboxylic acid tert-butyl ester

[0345] To a solution of methyl 5-(2-methoxycarbonyl-vinyl)-indole-1-carboxylic acid tert-butyl ester (4.64 g, 15.3 mmol, 1.0 eq.) in THF (87 mL) at −30° C. was added LiAlH₄ (I N in THF, 18.6 mL, 1.2 eq.) by syringe pump over 20 min and the resulting mixture was stirred and warmed to −5° C. After cooling back to −30° C., the reaction was then quenched by slow addition of acetone (10 mL) keeping temperature below −15° C., poured into Rochelle salt at 0° C., stirred for 1 h and the separated aqueous layer was extracted with EtOAc. The combunede organic phase was dried over sodium sulfate, filtered and concentrated. The residue was purification by column chromatography (methylene chloride to 2% acetone/methylene chloride) to give 5-(3-hydroxy-propenyl)-indole-1-carboxylic acid tert-butyl ester (2.89 g, 70%) or or similarly 6-(3-hydroxy-propenyl)-indole-1-carboxylic acid tert-butyl ester.

[0346] 5-(3-morpholin-4-yl-propenyl)-indole-1-carboxylic acid tert-butyl ester or 6-(3-morpholin-4-yl-propenyl)-indole-1-carboxylic acid tert-butyl ester

[0347] To a solution 5-(3-hydroxy-propenyl)-indole-1-carboxylic acid tert-butyl ester (0.95 mg, 3.48 mmol, 1.0 eq.) and Et₃N (1.8 mL, 3.0 eq.) in methylene chloride (10 mL) at 0° C. was added MsCl (0.40 mL, 1.5 eq.). The resulting mixture was stirred for 30 min and wormed to room temperature and stirred for additional 1 h. Then cyclohexyl-methyl-amine (8.3 mL, 18 eq.) was introduced and the resulting mixture was stirred over weekend, diluted with sat. NaHCO₃ and the separated aqueous phase was extracted with 3×EtOAc. The combined organic phase was dried over Na₂SO₄, filtered and concentrated. The residue was purified by silica gel chromatography (50% EtOAc/hexanes) to give 5-(3-morpholin-4-yl-propenyl)-indole-1-carboxylic acid tert-butyl ester or similarly 6-(3-morpholin-4-yl-propenyl)-indole-1-carboxylic acid tert-butyl ester.

[0348] Analogs ER-808501, ER-808514, ER-8085042 and ER-808544 are prepared from 5-(2-morpholin-4-yl-ethyl)-indole-1-carboxylic acid tert-butyl ester, 5-(3-morpholin-4-yl-propenyl)-indole-1-carboxylic acid tert-butyl ester, 6-(3-morpholin-4-yl-propenyl)-indole-1-carboxylic acid tert-butyl ester and 6-(2-morpholin-4-yl-ethyl)-indole-1-carboxylic acid tert-butyl ester following the same procedures for the preparation of 16 from 14.

[0349] A solution of 20 (51 mg) in methylene chloride (1 mL) was treated at room temperature with trifluoroacetic acid (1 mL) for 3 h and concentrated. The solid residue was washed with Et₂O and MeOH to give crude product (18.2 mg). The crude product was then purified by reverse phase HPLC (MeOH-water) to give ER-809047 (9.6 mg, 44%). MS (ES), ¹⁹F and ¹HNMR confirmed the structure.

[0350] A mixture of 7-chloro-3H-imidazo[4,5-b]pyridine (J. Heterocyclic. Chem. 1982, 19, 513) (250 mg, contain 25% of 5-chloro-3H-imidazo[4,5-b]pyridine), 2-tributylstannanyl-indole-1-carboxylic acid tert-butyl ester (11, 822 mg) and tetrakis(triphenyphosphine)palladium(0) (188 mg) in DMF (10 mL) was heated at 120° C. for 6 h. The reaction mixture was extracted with AcOEt, and washed with water and brine. Organic layer was dried over MgSO₄ and evaporated. The residue was purified by chromatography (AcOEt/hexane) to give 7-(1H-indol-2-yl)-3H-imidazo[4,5-b]pyridine IC-261 (28 mg) as a pale brown solid. ¹H NMR confirmed the structure.

[0351] A mixture of 2 (1.66 g, 6 mmol), 2-tributylstannanyl-indole-1-carboxylic acid tert-butyl ester (11, 3.6 g, 7 mmol), triethylamine (0.83 ml, 6 mmol), and tetrakis(triphenylphosphine)palladium(0) (600 mg, 10 mol %) in DMF (10 mL) was heated at 130° C. for 6 h. During the reaction, 11 was added in two portions (1.01 g×2). The reaction mixture was extracted with ethyl acetate and washed with water, and dried over anhydrous magnesium sulfate. After filtration, silica gel (400 mesh) was added to the residue and concentrated. The residue was purified by chromatography (AcOEt/MeOH) to give IC-395 (240 mg) and IC-375 (80 mg). ¹H NMR confirmed the structure.

[0352] (7-chloro-2-oxo-2,3-dihydro-1H-imidazo[4,5-b]pyridin-5-yl)-carbamic acid ethyl ester

[0353] To a solution of diethyl 4-chloro-5-nitro-2,6-pyridinedicarbamate (intermediate for the preparation of 1) (500 mg) in EtOH (50 mL) was added Raney Ni (1 g) and stirred for 12 h under hydrogen atmosphere at room temperature. Reaction mixture was filtered on celite and filtrate was concentrated under reduced pressure. Residue was dissolved in 2-propanol (10 mL) and stirred for 60 h under reflux. The reaction mixture was cooled to room temperature and precipitate was filtered. The filtrate was concentrated to give 250 mg of (7-chloro-2-oxo-2,3-dihydro-1H-imidazo[4,5-b]pyridin-5-yl)-carbamic acid ethyl ester as a gray solid. ¹H NMR confirmed the structure.

[0354] A mixture of (7-chloro-2-oxo-2,3-dihydro-1H-imidazo[4,5-b]pyridin-5-yl)-carbamic acid ethyl ester (240 mg), 2-tributylstannanyl-indole-1-carboxylic acid tert-butyl ester (11, 472 mg) and tetrakis(triphenylphosphine)palladium(0) (54 mg) in DMF (10 mL) was heated at 120° C. for 4 h. Additional 2-tributylstannanyl-indole-1-carboxylic acid tert-butyl ester (11, 472 mg) and tetrakis(triphenylphosphine)palladium(0) (54 mg) was introduced and the resulting mixture was heated at 120° C. for an additional 12 h. The reaction mixture was concentrated under reduced pressure and purified by chromatography (AcOEt/MeOH) to give IC-380 (20 mg) as a pale gray solid. ¹H NMR confirmed the structure.

[0355] (2-amino-7-chloro-3H-imidazo[4,5-b]pyridin-5-yl)-carbamic acid ethyl ester

[0356] Cyanogen bromide (0.55 g, 5.2 mmol) was added to a stirred solution of ethyl 5,6-diamino-4-chloro-2-pyridinecarbamate (intermediate for the preparation of 1, 1.00 g, 4.3 mmol) in 20 mL of ethanol at room temperature. The solution was stirred for 3 h and then at 60° C. for 3 h. The precipitate was filtered and washed with diethyl ether to give (2-amino-7-chloro-3H-imidazo[4,5-b]pyridin-5-yl)-carbamic acid ethyl ester (0.55 g, 38%) as a yellow powder. ¹H NMR confirmed the structure.

[0357] IC-416 was obtained from (2-amino-7-chloro-3H-imidazo[4,5-b]pyridin-5-yl)-carbamic acid ethyl ester and 11 by using the typical procedure described for IC-380. ¹H NMR confirmed the structure.

[0358] 7-iodo-2-alkyl-3H-imidazo [4,5-b]pyridine

[0359] Compound 7-iodo-2-alkyl-3H-imidazo[4,5-b]pyridine (7-iodo-3H-imidazo[4,5-b]pyridine, 7-iodo-2-methyl-3H-imidazo[4,5-b]pyridine, 7-iodo-2-ethyl-3H-imidazo[4,5-b]pyridine) and/or its HI salt was prepared from 4-chloro-pyridine-2,3-diamine (Recueil, 1969, 88, 1263-1274) following the same procedure for the preparation of 2 and 4 from 1.

[0360] 5-fluoro-7-iodo-2-methyl-3H-imidazo[4,5-b]pyridine

[0361] To a solution of 4 (R₂=Me, HI mono-salt, 300 mg, 0.75 mmol, 1.0 eq.) in HBF₄ (48-51% in water, 3 mL) at 0° C. was added NaNO2 (1.0 g, 19 eq.) portionwise over 1 h period keeing the reaction temperature under 4° C. The resulting mixture was stirred at 0° C. for 40 min and at room temperature for 30 min. The reaction was then quenched with sat. NaHCO₃ and the resulting mixture was extracted with 5×Et₂O. The combined organic phase was dried over Na₂SO₄, filtered and concentrated to give 5-fluoro-7-iodo-2-methyl-3H-imidazo[4,5-b]pyridine as a light brown solid (170 mg, 86%). ¹⁹FNMR, ¹HNMR and MS confirmed the structure.

[0362] Compound 66 was prepared from 7-iodo-2-alkyl-3H-imidazo[4,5-b]pyridine (or its HI mono-salt) or 5-fluoro-7-iodo-2-methyl-3H-imidazo[4,5-b]pyridine and 15 following the same procedure for the preparation of 13 or 64.

[0363] Compound 67 was prepared from 7-iodo-2-methyl-3H-imidazo[4,5-b]pyridine and 15 following the same procedure for the preparation of 65. ¹H NMR ER-# 1. Structure of 66 or 67 and/or MS 807496

¹H NMR 807584

¹H NMR 807585

¹H NMR 807587

¹H NMR 807750

¹H NMR 807787

¹H NMR 807788

¹H NMR 807865

¹H NMR 808009

¹H NMR 808081

¹H NMR 808085

¹H NMR 808160

¹H NMR 808256

¹H NMR 808257

¹H NMR 808259

¹H NMR 808260

¹H NMR 808261

¹H NMR 808262

¹H NMR 808266

¹H NMR 808268

¹H NMR 808269

¹H NMR 808284

¹H NMR 808285

¹H NMR 808286

¹H NMR 808287

¹H NMR 808288

¹H NMR 808289

¹H NMR 808291

¹H NMR 808310

¹H NMR 808311

¹H NMR 808319

¹H NMR 808322

¹H NMR 808361

¹H NMR 808362

¹H NMR 808363

¹H NMR 808370

¹H NMR 808372

¹H NMR 808385

¹H NMR 808386

¹H NMR 808388

¹H NMR 808469

¹H NMR 808470

¹H NMR 808473

¹H NMR 808496

¹H NMR 808497

¹H NMR 808498

¹H NMR 808499

¹H NMR 808500

¹H NMR 808513

¹H NMR 808541

¹H NMR 808543

¹H NMR 808571

¹H NMR 808600

¹H NMR 808617

¹H NMR 808620

¹H NMR 808622

¹H NMR 808623

¹H NMR 808624

¹H NMR 808628

¹H NMR 808629

¹H NMR 808631

¹H NMR 808635

¹H NMR 808636

¹H NMR 808637

¹H NMR 808660

¹H NMR 808672

¹H NMR 808673

¹H NMR 808691

¹H NMR 808692

¹H NMR 808703

¹H NMR 808704

¹H NMR 808705

¹H NMR 808711

¹H NMR 808712

¹H NMR 808713

¹H NMR 808714

¹H NMR 808717

¹H NMR 808719

¹H NMR 808720

¹H NMR 808834

¹H NMR 808835

¹H NMR 808849

¹H NMR 809187

¹H NMR 809196

MS 809197

MS 809198

MS 809199

MS 809200

MS 809201

MS 809202

MS 809203

MS 809204

MS 809205

MS 809206

MS 809207

MS 809208

MS 809209

MS 809210

MS 809211

MS 809212

MS 809213

MS 809214

MS 809215

MS 809216

MS 809217

MS 809218

MS 809219

MS 809220

MS 809221

MS 809222

MS 809223

MS 809224

MS 809225

MS 809226

MS 809227

MS 809228

MS 809229

MS 809230

MS 809231

MS 809232

MS 809233

MS 809234

MS 809235

MS 809236

MS 809237

MS 809238

MS

[0364] 7-iodo-2-methyl-1,4-dihydro-imidazo[4,5-b]pyridin-5-one

[0365] To a solution of compound 4 (R=Me, 160 mg, 0.59 mmol) in 10 mL of 20% aqueous H₂SO₄ at 0° C. was added sodium nitrite (1.54 mmol) in small portions and the resulting mixture was stirred at room temperature overnight. The reaction mixture was neutralized with sat. aqueous NH₃ to pH 7-8, and the resulting precipitate was collected to give a yellow solid. This solid was then crystallized in water to give 140 mg of product 7-iodo-2-methyl-1,4-dihydro-imidazo[4,5-b]pyridin-5-one (87%) with satisfactory MS and ¹H NMR.

[0366] ER-807546 was prepared from 7-iodo-2-methyl-1,4-dihydro-imidazo[4,5-b]pyridin-5-one and 10 (R′=PhCH₂, R″=Me) following the same procedure for the preparation of 13. Satisfactory MS and ¹H NMR were obtained for ER-807546.

[0367] Analogs ER-809251 and ER-809252 are prepared from 7-iodo-2-methyl-3H-imidazo[4,5-b]pyridine and 6-[2-(cyclohexyl-methyl-amino)-ethyl]-indole-1-carboxylic acid tert-butyl ester and 5-[2-(cyclohexyl-methyl-amino)-ethyl]-indole-1-carboxylic acid tert-butyl ester respectively following the same procedures for the preparation of 16 from 14.

[0368] 3) Biological Assays

[0369] HUVEC Assay Protocol:

[0370] Pooled human umbilical vein endothelial cells (HUVEC, Clonetics, Inc) were seeded in 96 well plates at 5×10⁴ cell/ml and incubated at 37° C. The following day, 20 μl of the each compound dilution was added to the cells and incubated for 30 minutes followed by stimulation with TNFα (1 ng/ml) for four hours at 37° C. After TNF stimulation, the plates were washed with PBS containing 0.5% BSA, fixed with 0.025% glutaraldehyde, and stained with primary and secondary antibodies for detection of E-selectin and ICAM expression. The plates were incubated with 100 μl of the primary murine anti-human E-selectin and anti-human ICAM antibody (R&D Systems, Minneapolis, Minn.) diluted 1:500 in PBS containing 0.5% BSA and 5% FBS for one hour after which the plates were washed and incubated with 100 μl of a secondary peroxidase conjugated goat anti-mouse IgG antibody (Pierce, Rockford, Ill.) diluted 1:10,000 in PBS/0.5% BSA/5% FBS for 30 minutes. The plates were then washed and 100 μl of TMB substrate was added and the color reaction was allowed to develop for 15-20 minutes. The reaction was stopped by the addition of 50 μl of 1 N H₂SO₄ and the optical density (OD) was read on microplate spectrophotometer at 450 nm. IC₅₀ values were determined based on percent inhibition as calculated by the following formula: ${\% \quad {Inhibition}} = {\left( {1 - \left( \frac{\left( {{{{avg}.\quad {compound}}\quad {OD}} - {{{avg}.\quad {blank}}\quad {OD}}} \right)}{\left( {{{{avg}.\quad {TNF}}\quad {OD}} - {{{avg}.\quad {blank}}\quad {OD}}} \right)} \right)} \right)*100}$ 

What is claimed is:
 1. A method for treating or lessening the severity of reperfusion injuries, osteoporosis and/or bone metastasis comprising: administering to a subject in need thereof a therapeutically effective amount of a compound having the structure (I):

or pharmaceutically acceptable derivative thereof; wherein n is an integer from 0-4; R₁ is hydrogen, —NH₂, —NHMe, —NHAc, —OH, F, —OMe, —CN, or —NH(C═O)OEt; R₂ is hydrogen, —NR_(A)R_(B), —OR_(A), an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, wherein R_(A) and R_(B) are each independently hydrogen or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety; each occurrence of R₃ is independently hydrogen, halogen, cyano, or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or a group —G—R_(C), wherein G is absent or is —CH₂—, —NR_(D)—, —O—, or (C═O), and wherein R_(C) is hydrogen, —NR_(F)R_(G), —OR_(F), —SR_(F), or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, wherein R_(D), R_(F) and R_(G) are each independently hydrogen, —NR_(x)R_(y), an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(D) and R_(C) or R_(F) and R_(G) taken together are a 3-, 4-, 5-, 6-, 7- or 8-membered substituted or unsubstituted cycloaliphatic or cycloheteroaliphatic moiety; wherein each occurrence of R_(x) and R_(y) is independently hydrogen, an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(x) and R_(y) taken together are a 4-, 5- or 6-membered substituted or unsubstituted, saturated or unsaturated cycloaliphatic or cycloheteroaliphatic moiety; and a pharmaceutically acceptable carrier or diluent; and optionally further comprising administering an additional therapeutic agent.
 2. The method of claim 1, wherein the compound has the structure:

wherein R_(3a) and R_(3b) are each independently hydrogen, halogen, cyano, or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or a group —G—R_(C), wherein G is absent, —CH₂—, —NR_(D)—, —O—, or (C═O), and wherein R_(C) is hydrogen, —NR_(F)R_(G), —OR_(F), —SR_(F), or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, wherein R_(D), R_(F) and R_(G) are each independently hydrogen, —NR_(x)R_(y), an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(D) and R_(C) or R_(F) and R_(G) taken together are a 3-, 4-, 5-, 6-, 7- or 8-membered substituted or unsubstituted cycloaliphatic or cycloheteroaliphatic moiety; wherein each occurrence of R_(x) and R_(y) is independently hydrogen, an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(x) and R_(y) taken together are a 4-, 5- or 6-membered substituted or unsubstituted, saturated or unsaturated cycloaliphatic or cycloheteroaliphatic moiety.
 3. The method of claim 1, wherein the compound has the structure:

wherein R_(3a) and R_(3b) are each independently hydrogen, halogen, cyano, or an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or a group —G—R_(C), wherein G is absent, —CH₂—, —NR_(D)—, —O—, or (C═O), and wherein R_(C) is hydrogen, —NR_(F)R_(G), —OR_(F), —SR_(F), or an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, wherein R_(D), R_(F) and R_(G) are each independently hydrogen, —NR_(x)R_(y), an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(D) and R_(C) or R_(F) and R_(G) taken together are a 3-, 4-, 5-, 6-, 7- or 8-membered substituted or unsubstituted cycloaliphatic or cycloheteroaliphatic moiety; wherein each occurrence of R_(x) and R_(y) is independently hydrogen, an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety, an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety, or wherein R_(x), and R_(y) taken together are a 4-, 5- or 6-membered substituted or unsubstituted, saturated or unsaturated cycloaliphatic or cycloheteroaliphatic moiety.
 4. The method of claim 1, wherein the compound has the structure:

wherein R₁, R₂, R_(F) and R_(G) are as defined in claim
 1. 5. The method of claim 1, wherein the compound has the structure:

wherein R₁, R₂, R_(F) and R_(G) are as defined in claim
 1. 6. The method of claim 1, wherein the compound has the structure:

wherein R₁, R₂, R_(F) and R_(G) are as defined in claim
 1. 7. The method of claim 1, wherein the compound has the structure:

wherein q and r are each independently 0 or 1; and R₁, R₂, R_(F) and R_(G) are as defined in claim
 1. 8. The method of claim 1, wherein the compound has the structure:

wherein q and r are each independently 0 or 1; and R₁, R₂, R_(F) and R_(G) are as defined in claim
 1. 9. The method of claim 1, wherein the compound has the structure:

wherein R₁, R₂, R_(F) and R_(G) are as defined in claim
 1. 10. The method of claim 1, wherein the compound has the structure:

wherein R₁, R₂, R_(F) and R_(G) are as defined in claim
 1. 11. The method of claim 1, wherein the compound has the structure:

wherein R₁ and R₂ are as defined in claim 1; m is 0, 1 or 2; and R_(F) is an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety.
 12. The method of claim 1, wherein the compound has the structure:

wherein R₁ and R₂ are as defined in claim 1; and R_(F) is hydrogen, a protective group or an aliphatic, cycloaliphatic, heteroaliphatic, cycloheteroaliphatic, aryl, or heteroaryl moiety.
 13. The method of claim 1, wherein the compound has the structure:

wherein R₁ and R₂ are as defined in claim 1; G is CH₂ or —(C═O); and X is O, S, C═O, S═O, C═CR₄R₅, NR₄, or CR₄R₅; wherein each occurrence of R₄ and R₅ is independently hydrogen, hydroxyl, halogen, cyano an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, or is an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety.
 14. The method of claim 1, wherein the compound has the structure:

wherein R₁ and R₂ are as defined in claim 1; G is CH₂ or —(C═O); and X is O, S, C═O, S═O, C═CR₄R₅, NR₄, or CR₄R₅; wherein each occurrence of R₄ and R₅ is independently hydrogen, hydroxyl, halogen, cyano an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, or is an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety.
 15. The method of claim 1, wherein the compound has the structure:

wherein R₁ and R₂ are as defined in claim 1; G is CH₂ or —(C═O); and X is O, S, C═O, S═O, C═CR₄R₅, NR₄, or CR₄R₅; wherein each occurrence of R₄ and R₅ is independently hydrogen, hydroxyl, halogen, cyano an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, or is an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety.
 16. The method of claim 1, wherein the compound has the structure:

wherein R₁ and R₂ are as defined in claim 1; p is an integer from 0-3; s is an integer from 0-4; A, B, D, E and each occurrence of K are independently absent, O, S, —C═O, —S═O, —C═CR₄R₅, —NR₄, or —CR₄R₅, wherein each occurrence of R₄ and R₅ is independently hydrogen, hydroxyl, halogen, cyano, —OR_(x), —SR_(x), —NR_(x)R_(y), an aliphatic, heteroaliphatic, aryl, or heteroaryl moiety, or is an acyl moiety substituted with an aliphatic, heteroaliphatic, aryl or heteroaryl moiety; and wherein A and B, B and D, D and E, E and K and any two adjacent K groups may be linked by a single or double bond as valency permits; wherein each occurrence of R_(x) and R_(y) is independently hydrogen, a protecting group, or an aliphatic, heteroaliphatic, aryl, heteroaryl, aliphaticaryl, heteroaliphatic aryl, aliphaticheteroaryl or heteroaliphaticheteroaryl moiety.
 17. The method of any one of claims 1-16, wherein in the compound R₁ is NH₂.
 18. The method of any one of claims 1-16, wherein in the compound R₁ is hydrogen.
 19. The method of any one of claims 1-16, wherein in the compound R₂ is NH₂, OH, C₁-C₆ alkyl or C₁-C₆ alkenyl, said alkyl and alkenyl groups optionally substituted with halogen or hydroxyl.
 20. The method of any one of claims 1-16, wherein in the compound R₂ is C₁-C₂ alkyl.
 21. The method of any one of claims 1-16, wherein in the compound R₂ is methyl.
 22. The method of any one of claims 1-16, wherein in the compound R₂ is hydrogen.
 23. The method of any one of claims 4-10, wherein in the compound one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is an alkyl, heteroalkyl, aryl, heteroaryl, alkylaryl or alkylheteroaryl, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 3-, 4-, 5-, 6-, 7- or 8-membered substituted or unsubstituted, saturated or unsaturated cyclic or heterocyclic moiety.
 24. The method of any one of claims 4-10, wherein in the compound one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is an aryl, heteroaryl, alkylaryl or alkylheteroaryl moiety, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl, or wherein R_(F) and R_(G) taken together are a 3-, 4-, 5-, 6-, 7- or 8-membered substituted or unsubstituted, saturated or unsaturated cyclic or heterocyclic moiety.
 25. The method of claim 24, wherein in the compound one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is phenyl, pyridyl, (alkyl)phenyl, or (alkyl)pyridyl, optionally substituted with one or more occurrences of halogen, trifluromethoxy, methoxy, trifluoromethyl, methylthio, or substituted or unsubstituted lower alkyl, lower heteroalkyl, aryl or heteroaryl.
 26. The method of any one of claims 4-10, wherein in the compound one of R_(F) or R_(G) is hydrogen or lower alkyl; and the other is a cyclic or acyclic, linear or branched, saturated or unsaturated aliphatic moiety optionally substituted with one or more of substituted or unsubstituted aryl, heteroaryl, amide, alkoxy, hydroxyl, thioalkyl, thiol, acyl or amino.
 27. The method of claim 11, wherein in the compound R_(F) is an alkyl, cycloalkyl, heteroalkyl, cycloheteroalkyl, aryl, heteroaryl, alkylaryl or alkylheteroaryl, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl.
 28. The method of claim 12, wherein in the compound R_(F) is hydrogen, a protecting group, or an alkyl, cycloalkyl, heteroalkyl, cycloheteroalkyl, aryl, heteroaryl, alkylaryl or alkylheteroaryl, optionally independently substituted for each occurrence with one or more of halogen, alkoxy, thioalkyl, or substituted or unsubstituted alkyl, heteroalkyl, aryl, or heteroaryl. 